Starting phenix.real_space_refine on Thu Feb 5 21:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi2_40060/02_2026/8gi2_40060.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.124 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 60 5.16 5 C 12780 2.51 5 N 3400 2.21 5 O 4580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 2.02, per 1000 atoms: 0.10 Number of scatterers: 20820 At special positions: 0 Unit cell: (117.72, 117.72, 197.64, 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 60 16.00 O 4580 8.00 N 3400 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 19.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL C 25 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL D 25 " --> pdb=" O PRO D 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL F 25 " --> pdb=" O PRO F 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL G 25 " --> pdb=" O PRO G 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL H 25 " --> pdb=" O PRO H 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL I 25 " --> pdb=" O PRO I 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL J 25 " --> pdb=" O PRO J 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE J 34 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL K 25 " --> pdb=" O PRO K 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL M 25 " --> pdb=" O PRO M 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL O 25 " --> pdb=" O PRO O 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL P 25 " --> pdb=" O PRO P 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL S 25 " --> pdb=" O PRO S 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE S 34 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL T 25 " --> pdb=" O PRO T 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE T 34 " --> pdb=" O ALA T 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 58 through 63 Processing sheet with id=2, first strand: chain 'A' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA A 140 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN A 150 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 142 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 58 through 63 Processing sheet with id=4, first strand: chain 'B' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA B 140 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN B 150 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 142 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 58 through 63 Processing sheet with id=6, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA C 140 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN C 150 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE C 142 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG C 148 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 58 through 63 Processing sheet with id=8, first strand: chain 'D' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA D 140 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN D 150 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE D 142 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG D 148 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 58 through 63 Processing sheet with id=10, first strand: chain 'E' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA E 140 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN E 150 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE E 142 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG E 148 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 58 through 63 Processing sheet with id=12, first strand: chain 'F' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA F 140 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN F 150 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE F 142 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG F 148 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 58 through 63 Processing sheet with id=14, first strand: chain 'G' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA G 140 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLN G 150 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE G 142 " --> pdb=" O ARG G 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG G 148 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 58 through 63 Processing sheet with id=16, first strand: chain 'H' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA H 140 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN H 150 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE H 142 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG H 148 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'I' and resid 58 through 63 Processing sheet with id=18, first strand: chain 'I' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA I 140 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN I 150 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE I 142 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG I 148 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 58 through 63 Processing sheet with id=20, first strand: chain 'J' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA J 140 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN J 150 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE J 142 " --> pdb=" O ARG J 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG J 148 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'K' and resid 58 through 63 Processing sheet with id=22, first strand: chain 'K' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA K 140 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN K 150 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE K 142 " --> pdb=" O ARG K 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG K 148 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 58 through 63 Processing sheet with id=24, first strand: chain 'L' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA L 140 " --> pdb=" O GLN L 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN L 150 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE L 142 " --> pdb=" O ARG L 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG L 148 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'M' and resid 58 through 63 Processing sheet with id=26, first strand: chain 'M' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA M 140 " --> pdb=" O GLN M 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN M 150 " --> pdb=" O ALA M 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE M 142 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG M 148 " --> pdb=" O ILE M 142 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 58 through 63 Processing sheet with id=28, first strand: chain 'N' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA N 140 " --> pdb=" O GLN N 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN N 150 " --> pdb=" O ALA N 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE N 142 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG N 148 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'O' and resid 58 through 63 Processing sheet with id=30, first strand: chain 'O' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA O 140 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN O 150 " --> pdb=" O ALA O 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE O 142 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG O 148 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 58 through 63 Processing sheet with id=32, first strand: chain 'P' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA P 140 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN P 150 " --> pdb=" O ALA P 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE P 142 " --> pdb=" O ARG P 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG P 148 " --> pdb=" O ILE P 142 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'Q' and resid 58 through 63 Processing sheet with id=34, first strand: chain 'Q' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA Q 140 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN Q 150 " --> pdb=" O ALA Q 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE Q 142 " --> pdb=" O ARG Q 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG Q 148 " --> pdb=" O ILE Q 142 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 58 through 63 Processing sheet with id=36, first strand: chain 'R' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA R 140 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN R 150 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE R 142 " --> pdb=" O ARG R 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG R 148 " --> pdb=" O ILE R 142 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 58 through 63 Processing sheet with id=38, first strand: chain 'S' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA S 140 " --> pdb=" O GLN S 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN S 150 " --> pdb=" O ALA S 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE S 142 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG S 148 " --> pdb=" O ILE S 142 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 58 through 63 Processing sheet with id=40, first strand: chain 'T' and resid 82 through 87 removed outlier: 6.278A pdb=" N ALA T 140 " --> pdb=" O GLN T 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN T 150 " --> pdb=" O ALA T 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE T 142 " --> pdb=" O ARG T 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG T 148 " --> pdb=" O ILE T 142 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2340 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: 3.35 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4140 1.32 - 1.44: 4500 1.44 - 1.56: 12200 1.56 - 1.68: 0 1.68 - 1.80: 120 Bond restraints: 20960 Sorted by residual: bond pdb=" CA TYR F 127 " pdb=" CB TYR F 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR I 127 " pdb=" CB TYR I 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR O 127 " pdb=" CB TYR O 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR G 127 " pdb=" CB TYR G 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR J 127 " pdb=" CB TYR J 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 ... (remaining 20955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 26632 1.55 - 3.11: 1332 3.11 - 4.66: 316 4.66 - 6.22: 200 6.22 - 7.77: 100 Bond angle restraints: 28580 Sorted by residual: angle pdb=" N TYR T 127 " pdb=" CA TYR T 127 " pdb=" C TYR T 127 " ideal model delta sigma weight residual 112.93 106.41 6.52 1.12e+00 7.97e-01 3.39e+01 angle pdb=" N TYR J 127 " pdb=" CA TYR J 127 " pdb=" C TYR J 127 " ideal model delta sigma weight residual 112.93 106.42 6.51 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR E 127 " pdb=" CA TYR E 127 " pdb=" C TYR E 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR O 127 " pdb=" CA TYR O 127 " pdb=" C TYR O 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR M 127 " pdb=" CA TYR M 127 " pdb=" C TYR M 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.36e+01 ... (remaining 28575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.62: 11317 12.62 - 25.24: 763 25.24 - 37.85: 220 37.85 - 50.47: 80 50.47 - 63.09: 60 Dihedral angle restraints: 12440 sinusoidal: 4260 harmonic: 8180 Sorted by residual: dihedral pdb=" N SER S 131 " pdb=" C SER S 131 " pdb=" CA SER S 131 " pdb=" CB SER S 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N SER T 131 " pdb=" C SER T 131 " pdb=" CA SER T 131 " pdb=" CB SER T 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N SER R 131 " pdb=" C SER R 131 " pdb=" CA SER R 131 " pdb=" CB SER R 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 12437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2206 0.038 - 0.077: 935 0.077 - 0.115: 360 0.115 - 0.153: 119 0.153 - 0.191: 40 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CA SER K 130 " pdb=" N SER K 130 " pdb=" C SER K 130 " pdb=" CB SER K 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA SER Q 130 " pdb=" N SER Q 130 " pdb=" C SER Q 130 " pdb=" CB SER Q 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA SER R 130 " pdb=" N SER R 130 " pdb=" C SER R 130 " pdb=" CB SER R 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 3657 not shown) Planarity restraints: 3760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 117 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASN Q 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN Q 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA Q 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 117 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN N 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN N 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA N 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 117 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN M 117 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN M 117 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA M 118 " -0.021 2.00e-02 2.50e+03 ... (remaining 3757 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 29 2.18 - 2.86: 8124 2.86 - 3.54: 27383 3.54 - 4.22: 47858 4.22 - 4.90: 83245 Nonbonded interactions: 166639 Sorted by model distance: nonbonded pdb=" OE2 GLU M 146 " pdb=" OE1 GLU T 64 " model vdw 1.504 3.040 nonbonded pdb=" OE2 GLU I 146 " pdb=" OE1 GLU O 64 " model vdw 1.505 3.040 nonbonded pdb=" OE1 GLU A 64 " pdb=" OE2 GLU E 146 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU J 146 " pdb=" OE1 GLU P 64 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU A 146 " pdb=" OE1 GLU R 64 " model vdw 1.505 3.040 ... (remaining 166634 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: 0.09 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' } 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=0.00 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.008 0.076 20960 Z= 0.526 Angle : 0.975 7.771 28580 Z= 0.613 Chirality : 0.052 0.191 3660 Planarity : 0.004 0.037 3760 Dihedral : 11.484 63.089 7240 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.97 % Favored : 86.34 % Rotamer: Outliers : 3.45 % Allowed : 4.31 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.14), residues: 2900 helix: -1.19 (0.24), residues: 560 sheet: -0.76 (0.17), residues: 940 loop : -3.96 (0.10), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 148 TYR 0.007 0.001 TYR H 127 PHE 0.003 0.001 PHE P 159 HIS 0.002 0.001 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00758 (20960) covalent geometry : angle 0.97532 (28580) hydrogen bonds : bond 0.16360 ( 860) hydrogen bonds : angle 5.06380 ( 2340) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 646 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 127 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5314 (t80) REVERT: C 127 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.4616 (t80) REVERT: D 127 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.4625 (t80) REVERT: E 124 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4607 (p) REVERT: F 124 VAL cc_start: 0.4596 (OUTLIER) cc_final: 0.4235 (p) REVERT: F 143 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7978 (mt-10) REVERT: G 96 TYR cc_start: 0.6763 (t80) cc_final: 0.6061 (t80) REVERT: G 127 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5026 (t80) REVERT: H 63 ASP cc_start: 0.8019 (t0) cc_final: 0.7777 (t0) REVERT: H 96 TYR cc_start: 0.6884 (t80) cc_final: 0.6599 (t80) REVERT: H 112 ASP cc_start: 0.7873 (m-30) cc_final: 0.7494 (m-30) REVERT: H 127 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5030 (t80) REVERT: J 63 ASP cc_start: 0.8323 (t0) cc_final: 0.8081 (t0) REVERT: J 73 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8032 (mt-10) REVERT: K 96 TYR cc_start: 0.7253 (t80) cc_final: 0.7021 (t80) REVERT: K 127 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4957 (t80) REVERT: M 28 MET cc_start: 0.8702 (mmt) cc_final: 0.8447 (mmt) REVERT: M 73 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8076 (mt-10) REVERT: M 96 TYR cc_start: 0.7146 (t80) cc_final: 0.6869 (t80) REVERT: M 127 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5358 (t80) REVERT: N 63 ASP cc_start: 0.7739 (t0) cc_final: 0.7380 (t70) REVERT: N 127 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5196 (t80) REVERT: O 127 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5266 (t80) REVERT: P 129 LEU cc_start: 0.6516 (mt) cc_final: 0.6263 (mt) REVERT: R 127 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.4805 (t80) REVERT: R 129 LEU cc_start: 0.6056 (mt) cc_final: 0.5739 (mt) REVERT: S 94 THR cc_start: 0.6564 (t) cc_final: 0.6323 (m) REVERT: S 127 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.4818 (t80) REVERT: T 127 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4273 (t80) outliers start: 80 outliers final: 44 residues processed: 706 average time/residue: 0.5177 time to fit residues: 423.0523 Evaluate side-chains 626 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 568 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 119 ASN Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 126 ASN E 59 ASN F 93 GLN L 55 GLN L 126 ASN M 82 HIS N 126 ASN O 69 ASN P 69 ASN P 126 ASN Q 69 ASN R 126 ASN T 69 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.139328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112574 restraints weight = 28367.318| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.30 r_work: 0.3234 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20960 Z= 0.188 Angle : 0.691 13.476 28580 Z= 0.355 Chirality : 0.050 0.161 3660 Planarity : 0.003 0.023 3760 Dihedral : 7.184 82.495 3120 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 7.41 % Allowed : 14.18 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.15), residues: 2900 helix: 0.22 (0.22), residues: 580 sheet: -0.38 (0.18), residues: 960 loop : -3.59 (0.11), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.009 0.001 TYR F 127 PHE 0.019 0.002 PHE T 42 HIS 0.004 0.002 HIS O 82 Details of bonding type rmsd covalent geometry : bond 0.00446 (20960) covalent geometry : angle 0.69051 (28580) hydrogen bonds : bond 0.05877 ( 860) hydrogen bonds : angle 4.87906 ( 2340) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 562 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8084 (OUTLIER) cc_final: 0.7787 (m) REVERT: A 73 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8607 (mt-10) REVERT: A 90 ASP cc_start: 0.6467 (t0) cc_final: 0.6212 (t0) REVERT: A 127 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6396 (t80) REVERT: A 143 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 61 GLU cc_start: 0.7778 (pp20) cc_final: 0.7498 (pp20) REVERT: C 90 ASP cc_start: 0.7077 (t0) cc_final: 0.6730 (t0) REVERT: C 127 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6386 (t80) REVERT: C 133 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7974 (mt-10) REVERT: D 31 ILE cc_start: 0.9124 (mt) cc_final: 0.8834 (mp) REVERT: D 143 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8504 (mt-10) REVERT: F 90 ASP cc_start: 0.7058 (t0) cc_final: 0.6831 (OUTLIER) REVERT: F 143 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8573 (mt-10) REVERT: F 144 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: G 90 ASP cc_start: 0.6940 (t0) cc_final: 0.6712 (t0) REVERT: H 63 ASP cc_start: 0.8578 (t0) cc_final: 0.8332 (t0) REVERT: H 73 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8629 (mt-10) REVERT: I 90 ASP cc_start: 0.7292 (t0) cc_final: 0.6897 (t0) REVERT: J 63 ASP cc_start: 0.8757 (t0) cc_final: 0.8552 (t0) REVERT: J 73 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8578 (mt-10) REVERT: K 90 ASP cc_start: 0.7066 (t0) cc_final: 0.6837 (OUTLIER) REVERT: K 96 TYR cc_start: 0.7490 (t80) cc_final: 0.7126 (t80) REVERT: K 127 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.6282 (t80) REVERT: M 108 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8921 (mt) REVERT: M 148 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8438 (mtm180) REVERT: N 81 ASP cc_start: 0.8749 (m-30) cc_final: 0.8410 (m-30) REVERT: N 127 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6254 (t80) REVERT: N 143 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8547 (mt-10) REVERT: O 90 ASP cc_start: 0.6428 (t0) cc_final: 0.6143 (OUTLIER) REVERT: O 127 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6269 (t80) REVERT: P 61 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: Q 46 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8498 (tt) REVERT: Q 89 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8140 (mp) REVERT: R 127 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.5864 (t80) REVERT: S 127 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6179 (t80) REVERT: T 46 LEU cc_start: 0.8842 (tp) cc_final: 0.8612 (tt) REVERT: T 90 ASP cc_start: 0.5883 (t0) cc_final: 0.5647 (t0) REVERT: T 108 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8915 (mp) REVERT: T 123 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7604 (t) REVERT: T 144 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.8033 (tt0) outliers start: 172 outliers final: 77 residues processed: 629 average time/residue: 0.6055 time to fit residues: 430.2960 Evaluate side-chains 635 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 545 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 123 SER Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 144 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 209 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 220 optimal weight: 0.4980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 126 ASN E 59 ASN G 52 ASN L 55 GLN N 119 ASN P 119 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115012 restraints weight = 28391.136| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.31 r_work: 0.3266 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20960 Z= 0.129 Angle : 0.636 15.116 28580 Z= 0.318 Chirality : 0.048 0.153 3660 Planarity : 0.002 0.023 3760 Dihedral : 6.157 53.846 3058 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 6.90 % Allowed : 16.68 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.15), residues: 2900 helix: 0.77 (0.22), residues: 580 sheet: -0.04 (0.18), residues: 960 loop : -3.25 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 148 TYR 0.007 0.001 TYR F 127 PHE 0.014 0.001 PHE T 42 HIS 0.003 0.002 HIS Q 82 Details of bonding type rmsd covalent geometry : bond 0.00293 (20960) covalent geometry : angle 0.63605 (28580) hydrogen bonds : bond 0.04714 ( 860) hydrogen bonds : angle 4.66944 ( 2340) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 549 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8614 (mt-10) REVERT: A 90 ASP cc_start: 0.6872 (t0) cc_final: 0.6571 (t0) REVERT: A 127 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6330 (t80) REVERT: A 143 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8566 (mt-10) REVERT: B 103 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.5690 (p) REVERT: C 61 GLU cc_start: 0.7635 (pp20) cc_final: 0.7423 (pp20) REVERT: C 90 ASP cc_start: 0.7013 (t0) cc_final: 0.6577 (t0) REVERT: C 127 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6258 (t80) REVERT: C 133 GLU cc_start: 0.8221 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 31 ILE cc_start: 0.9060 (mt) cc_final: 0.8776 (mp) REVERT: D 127 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6137 (t80) REVERT: D 143 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8538 (mt-10) REVERT: E 26 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8922 (mm) REVERT: E 162 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7685 (mtpt) REVERT: F 90 ASP cc_start: 0.7427 (t0) cc_final: 0.7051 (t0) REVERT: F 133 GLU cc_start: 0.8629 (pm20) cc_final: 0.8085 (pt0) REVERT: G 90 ASP cc_start: 0.6993 (t0) cc_final: 0.6621 (t0) REVERT: G 103 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6406 (m) REVERT: H 63 ASP cc_start: 0.8529 (t0) cc_final: 0.8258 (t0) REVERT: H 73 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8661 (mt-10) REVERT: I 44 LEU cc_start: 0.9104 (mt) cc_final: 0.8895 (mt) REVERT: I 90 ASP cc_start: 0.7375 (t0) cc_final: 0.7043 (t0) REVERT: J 44 LEU cc_start: 0.9087 (mp) cc_final: 0.8810 (mt) REVERT: J 73 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8668 (mt-10) REVERT: K 90 ASP cc_start: 0.7025 (t0) cc_final: 0.6804 (t0) REVERT: K 96 TYR cc_start: 0.7417 (t80) cc_final: 0.6954 (t80) REVERT: K 127 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6209 (t80) REVERT: L 133 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: M 108 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8876 (mt) REVERT: N 90 ASP cc_start: 0.6535 (t0) cc_final: 0.6323 (t0) REVERT: N 96 TYR cc_start: 0.7549 (t80) cc_final: 0.6959 (t80) REVERT: N 127 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6283 (t80) REVERT: O 90 ASP cc_start: 0.6461 (t0) cc_final: 0.6118 (t0) REVERT: O 108 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8938 (mp) REVERT: O 127 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6165 (t80) REVERT: S 46 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8579 (tp) REVERT: S 133 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: T 90 ASP cc_start: 0.5984 (t0) cc_final: 0.5662 (t0) REVERT: T 108 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8895 (mp) outliers start: 160 outliers final: 82 residues processed: 609 average time/residue: 0.6107 time to fit residues: 420.4794 Evaluate side-chains 635 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 538 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 68 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 ASN I 126 ASN K 126 ASN L 55 GLN M 126 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127212 restraints weight = 27837.779| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.43 r_work: 0.3312 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20960 Z= 0.109 Angle : 0.625 16.068 28580 Z= 0.303 Chirality : 0.047 0.147 3660 Planarity : 0.002 0.024 3760 Dihedral : 5.918 53.877 3058 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.77 % Allowed : 18.19 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 2900 helix: 1.08 (0.22), residues: 580 sheet: 0.13 (0.19), residues: 960 loop : -2.97 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 148 TYR 0.005 0.001 TYR F 127 PHE 0.011 0.001 PHE T 42 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00233 (20960) covalent geometry : angle 0.62491 (28580) hydrogen bonds : bond 0.04169 ( 860) hydrogen bonds : angle 4.54567 ( 2340) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 546 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 126 ASN cc_start: 0.6202 (p0) cc_final: 0.5995 (p0) REVERT: A 127 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6335 (t80) REVERT: A 143 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8533 (mt-10) REVERT: B 103 THR cc_start: 0.6249 (OUTLIER) cc_final: 0.5633 (p) REVERT: C 61 GLU cc_start: 0.7599 (pp20) cc_final: 0.7374 (pp20) REVERT: C 90 ASP cc_start: 0.7013 (t0) cc_final: 0.6616 (t0) REVERT: C 127 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6049 (t80) REVERT: D 31 ILE cc_start: 0.9083 (mt) cc_final: 0.8829 (mp) REVERT: D 127 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6154 (t80) REVERT: D 143 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8537 (mt-10) REVERT: E 26 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8859 (mm) REVERT: E 90 ASP cc_start: 0.6311 (t0) cc_final: 0.5961 (p0) REVERT: E 162 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7671 (mtpt) REVERT: F 61 GLU cc_start: 0.8192 (tt0) cc_final: 0.7964 (tt0) REVERT: F 90 ASP cc_start: 0.7459 (t0) cc_final: 0.7036 (t0) REVERT: F 133 GLU cc_start: 0.8646 (pm20) cc_final: 0.8132 (pt0) REVERT: G 90 ASP cc_start: 0.7050 (t0) cc_final: 0.6756 (t0) REVERT: G 103 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6239 (m) REVERT: H 63 ASP cc_start: 0.8378 (t0) cc_final: 0.8143 (t0) REVERT: H 73 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8612 (mt-10) REVERT: I 44 LEU cc_start: 0.9041 (mt) cc_final: 0.8830 (mt) REVERT: I 90 ASP cc_start: 0.7326 (t0) cc_final: 0.7021 (t0) REVERT: J 44 LEU cc_start: 0.9020 (mp) cc_final: 0.8746 (mt) REVERT: J 73 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8709 (mt-10) REVERT: J 96 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6254 (t80) REVERT: J 127 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6294 (t80) REVERT: K 90 ASP cc_start: 0.6968 (t0) cc_final: 0.6743 (t0) REVERT: K 96 TYR cc_start: 0.7360 (t80) cc_final: 0.6842 (t80) REVERT: K 127 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.6290 (t80) REVERT: L 53 GLU cc_start: 0.7954 (tp30) cc_final: 0.7621 (tp30) REVERT: L 90 ASP cc_start: 0.6759 (t0) cc_final: 0.6371 (t0) REVERT: L 133 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: M 108 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8928 (mt) REVERT: N 90 ASP cc_start: 0.6566 (t0) cc_final: 0.6275 (t0) REVERT: N 96 TYR cc_start: 0.7634 (t80) cc_final: 0.6894 (t80) REVERT: N 127 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6255 (t80) REVERT: O 55 GLN cc_start: 0.8631 (mt0) cc_final: 0.8428 (mt0) REVERT: O 61 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: O 108 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8973 (mp) REVERT: O 127 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.6009 (t80) REVERT: P 127 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6063 (t80) REVERT: R 46 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8703 (tt) REVERT: S 94 THR cc_start: 0.7034 (OUTLIER) cc_final: 0.6628 (m) REVERT: S 133 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: T 101 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7577 (mmtm) outliers start: 157 outliers final: 73 residues processed: 607 average time/residue: 0.5570 time to fit residues: 383.5318 Evaluate side-chains 615 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 523 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 96 TYR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 106 optimal weight: 0.0770 overall best weight: 2.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN N 119 ASN O 119 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113325 restraints weight = 28369.812| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.27 r_work: 0.3244 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20960 Z= 0.199 Angle : 0.705 20.071 28580 Z= 0.341 Chirality : 0.050 0.168 3660 Planarity : 0.003 0.028 3760 Dihedral : 6.383 51.974 3058 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 8.36 % Allowed : 17.59 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 2900 helix: 1.10 (0.21), residues: 580 sheet: 0.04 (0.18), residues: 960 loop : -2.89 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.008 0.001 TYR F 127 PHE 0.010 0.002 PHE J 42 HIS 0.004 0.002 HIS P 82 Details of bonding type rmsd covalent geometry : bond 0.00486 (20960) covalent geometry : angle 0.70517 (28580) hydrogen bonds : bond 0.05597 ( 860) hydrogen bonds : angle 4.75436 ( 2340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 541 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8106 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 73 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8568 (mt-10) REVERT: A 90 ASP cc_start: 0.6574 (t0) cc_final: 0.6342 (t0) REVERT: A 127 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6351 (t80) REVERT: B 103 THR cc_start: 0.6449 (OUTLIER) cc_final: 0.5891 (p) REVERT: C 61 GLU cc_start: 0.7826 (pp20) cc_final: 0.7568 (pp20) REVERT: C 90 ASP cc_start: 0.7146 (t0) cc_final: 0.6691 (t0) REVERT: C 127 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6275 (t80) REVERT: D 31 ILE cc_start: 0.9142 (mt) cc_final: 0.8860 (mp) REVERT: D 90 ASP cc_start: 0.7062 (t0) cc_final: 0.6595 (t0) REVERT: D 143 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8617 (mt-10) REVERT: D 162 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7790 (mttt) REVERT: E 26 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8935 (mm) REVERT: E 93 GLN cc_start: 0.6018 (tm130) cc_final: 0.5639 (tm-30) REVERT: E 112 ASP cc_start: 0.8172 (m-30) cc_final: 0.7910 (m-30) REVERT: E 162 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7738 (mtpt) REVERT: F 90 ASP cc_start: 0.7549 (t0) cc_final: 0.7059 (t0) REVERT: F 133 GLU cc_start: 0.8742 (pm20) cc_final: 0.8230 (pt0) REVERT: G 90 ASP cc_start: 0.7258 (t0) cc_final: 0.6888 (t0) REVERT: G 144 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: H 63 ASP cc_start: 0.8563 (t0) cc_final: 0.8317 (t0) REVERT: H 73 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8614 (mt-10) REVERT: I 90 ASP cc_start: 0.7246 (t0) cc_final: 0.6694 (t0) REVERT: J 73 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8733 (mt-10) REVERT: K 127 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6179 (t80) REVERT: L 133 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: L 144 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: M 108 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8954 (mt) REVERT: N 26 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8926 (mm) REVERT: N 81 ASP cc_start: 0.8629 (m-30) cc_final: 0.8239 (m-30) REVERT: N 127 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6234 (t80) REVERT: N 143 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8678 (mt-10) REVERT: O 60 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7974 (mtt) REVERT: O 61 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: O 90 ASP cc_start: 0.6388 (t0) cc_final: 0.6108 (OUTLIER) REVERT: O 108 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8998 (mp) REVERT: O 127 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6103 (t80) REVERT: P 96 TYR cc_start: 0.7367 (t80) cc_final: 0.6572 (t80) REVERT: P 127 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.5855 (t80) REVERT: Q 89 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8184 (mp) outliers start: 194 outliers final: 97 residues processed: 621 average time/residue: 0.5562 time to fit residues: 392.0024 Evaluate side-chains 639 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 525 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 135 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 254 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114128 restraints weight = 28148.418| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.26 r_work: 0.3233 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20960 Z= 0.181 Angle : 0.709 19.167 28580 Z= 0.340 Chirality : 0.050 0.161 3660 Planarity : 0.003 0.029 3760 Dihedral : 6.353 54.908 3056 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 7.84 % Allowed : 18.92 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 2900 helix: 1.13 (0.21), residues: 580 sheet: 0.01 (0.18), residues: 960 loop : -2.85 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.008 0.001 TYR F 127 PHE 0.008 0.001 PHE T 42 HIS 0.003 0.002 HIS P 82 Details of bonding type rmsd covalent geometry : bond 0.00444 (20960) covalent geometry : angle 0.70929 (28580) hydrogen bonds : bond 0.05351 ( 860) hydrogen bonds : angle 4.73455 ( 2340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 531 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7793 (m) REVERT: A 31 ILE cc_start: 0.9276 (mp) cc_final: 0.9028 (mp) REVERT: A 73 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8587 (mt-10) REVERT: A 90 ASP cc_start: 0.6662 (t0) cc_final: 0.6373 (t0) REVERT: A 127 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 148 ARG cc_start: 0.8833 (mtp85) cc_final: 0.8595 (mtm180) REVERT: B 103 THR cc_start: 0.6322 (OUTLIER) cc_final: 0.5716 (p) REVERT: C 61 GLU cc_start: 0.7886 (pp20) cc_final: 0.7600 (pp20) REVERT: C 90 ASP cc_start: 0.7034 (t0) cc_final: 0.6625 (t0) REVERT: C 93 GLN cc_start: 0.6326 (tm130) cc_final: 0.6038 (tm-30) REVERT: C 127 TYR cc_start: 0.7663 (OUTLIER) cc_final: 0.6546 (t80) REVERT: D 31 ILE cc_start: 0.9100 (mt) cc_final: 0.8856 (mp) REVERT: D 90 ASP cc_start: 0.7124 (t0) cc_final: 0.6801 (t0) REVERT: D 143 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8583 (mt-10) REVERT: D 162 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7866 (mttt) REVERT: E 26 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8910 (mm) REVERT: E 93 GLN cc_start: 0.6021 (tm130) cc_final: 0.5778 (tm-30) REVERT: E 112 ASP cc_start: 0.8151 (m-30) cc_final: 0.7882 (m-30) REVERT: E 162 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7733 (mtpt) REVERT: F 90 ASP cc_start: 0.7551 (t0) cc_final: 0.6898 (t0) REVERT: F 133 GLU cc_start: 0.8696 (pm20) cc_final: 0.8202 (pt0) REVERT: G 59 ASN cc_start: 0.8989 (t0) cc_final: 0.8710 (t0) REVERT: G 90 ASP cc_start: 0.7282 (t0) cc_final: 0.6971 (t0) REVERT: G 144 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: H 63 ASP cc_start: 0.8575 (t0) cc_final: 0.8333 (t0) REVERT: H 73 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 90 ASP cc_start: 0.7282 (t0) cc_final: 0.6655 (t0) REVERT: J 73 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8646 (mt-10) REVERT: K 127 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6182 (t80) REVERT: L 133 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: L 144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: M 108 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8954 (mt) REVERT: N 26 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8926 (mm) REVERT: N 96 TYR cc_start: 0.7635 (t80) cc_final: 0.7061 (t80) REVERT: N 127 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6239 (t80) REVERT: N 143 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8692 (mt-10) REVERT: O 61 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: O 108 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8984 (mp) REVERT: P 127 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.5891 (t80) REVERT: S 133 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8099 (mp0) outliers start: 182 outliers final: 102 residues processed: 605 average time/residue: 0.5643 time to fit residues: 385.6408 Evaluate side-chains 639 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 521 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 135 THR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 249 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN O 126 ASN P 55 GLN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119636 restraints weight = 27982.924| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.36 r_work: 0.3253 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20960 Z= 0.163 Angle : 0.696 18.865 28580 Z= 0.334 Chirality : 0.049 0.158 3660 Planarity : 0.003 0.028 3760 Dihedral : 6.216 55.660 3054 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.41 % Allowed : 19.35 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 2900 helix: 1.30 (0.21), residues: 540 sheet: 0.01 (0.18), residues: 960 loop : -2.82 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.007 0.001 TYR F 127 PHE 0.007 0.001 PHE T 42 HIS 0.003 0.002 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00394 (20960) covalent geometry : angle 0.69595 (28580) hydrogen bonds : bond 0.05138 ( 860) hydrogen bonds : angle 4.69526 ( 2340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 528 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (m) REVERT: A 31 ILE cc_start: 0.9265 (mp) cc_final: 0.9048 (mp) REVERT: A 73 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8600 (mt-10) REVERT: A 90 ASP cc_start: 0.6695 (t0) cc_final: 0.6419 (t0) REVERT: A 127 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 148 ARG cc_start: 0.8843 (mtp85) cc_final: 0.8604 (mtm180) REVERT: B 90 ASP cc_start: 0.7270 (t0) cc_final: 0.6982 (t0) REVERT: B 103 THR cc_start: 0.6191 (OUTLIER) cc_final: 0.5581 (p) REVERT: C 61 GLU cc_start: 0.7920 (pp20) cc_final: 0.7592 (pp20) REVERT: C 90 ASP cc_start: 0.6928 (t0) cc_final: 0.6545 (t0) REVERT: C 93 GLN cc_start: 0.6347 (tm130) cc_final: 0.6040 (tm-30) REVERT: C 127 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6539 (t80) REVERT: D 31 ILE cc_start: 0.9081 (mt) cc_final: 0.8836 (mp) REVERT: D 90 ASP cc_start: 0.7180 (t0) cc_final: 0.6828 (t0) REVERT: D 143 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8593 (mt-10) REVERT: D 162 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7837 (mttt) REVERT: E 26 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8898 (mm) REVERT: E 112 ASP cc_start: 0.8192 (m-30) cc_final: 0.7896 (m-30) REVERT: E 162 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7674 (mtpt) REVERT: F 127 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: F 133 GLU cc_start: 0.8714 (pm20) cc_final: 0.8175 (pt0) REVERT: F 144 GLU cc_start: 0.8798 (pt0) cc_final: 0.8562 (pt0) REVERT: G 90 ASP cc_start: 0.7273 (t0) cc_final: 0.6942 (t0) REVERT: G 144 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: H 63 ASP cc_start: 0.8462 (t0) cc_final: 0.8225 (t0) REVERT: H 73 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8624 (mt-10) REVERT: I 61 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8200 (mt-10) REVERT: I 90 ASP cc_start: 0.7334 (t0) cc_final: 0.6707 (t0) REVERT: J 44 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8950 (mt) REVERT: J 73 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8667 (mt-10) REVERT: K 127 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6176 (t80) REVERT: L 61 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7354 (pp20) REVERT: L 133 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: L 144 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: M 108 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8930 (mt) REVERT: N 26 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8852 (mm) REVERT: N 93 GLN cc_start: 0.7082 (mt0) cc_final: 0.6840 (pt0) REVERT: N 96 TYR cc_start: 0.7623 (t80) cc_final: 0.6872 (t80) REVERT: N 127 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6128 (t80) REVERT: N 143 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8730 (mt-10) REVERT: O 61 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: O 108 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8942 (mp) REVERT: P 127 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.5804 (t80) REVERT: S 133 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8182 (mp0) outliers start: 172 outliers final: 96 residues processed: 600 average time/residue: 0.6060 time to fit residues: 411.2680 Evaluate side-chains 631 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 516 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 23 ILE Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 135 THR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 192 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN E 126 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN L 119 ASN M 119 ASN N 119 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 ASN ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 126 ASN T 93 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121143 restraints weight = 28012.716| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.36 r_work: 0.3228 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20960 Z= 0.118 Angle : 0.676 23.043 28580 Z= 0.319 Chirality : 0.048 0.158 3660 Planarity : 0.002 0.027 3760 Dihedral : 5.679 56.896 3050 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.12 % Allowed : 21.21 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 2900 helix: 1.60 (0.21), residues: 520 sheet: 0.13 (0.18), residues: 960 loop : -2.83 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 148 TYR 0.005 0.001 TYR J 156 PHE 0.007 0.001 PHE T 42 HIS 0.003 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00265 (20960) covalent geometry : angle 0.67585 (28580) hydrogen bonds : bond 0.04270 ( 860) hydrogen bonds : angle 4.53079 ( 2340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 529 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8936 (mp) REVERT: A 73 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 96 TYR cc_start: 0.7117 (t80) cc_final: 0.6706 (t80) REVERT: A 127 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6241 (t80) REVERT: A 143 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8560 (mt-10) REVERT: B 90 ASP cc_start: 0.7166 (t0) cc_final: 0.6865 (t0) REVERT: B 103 THR cc_start: 0.5999 (OUTLIER) cc_final: 0.5399 (p) REVERT: C 61 GLU cc_start: 0.7601 (pp20) cc_final: 0.7264 (pp20) REVERT: C 90 ASP cc_start: 0.6944 (t0) cc_final: 0.6562 (t0) REVERT: C 93 GLN cc_start: 0.6025 (tm130) cc_final: 0.5714 (tm-30) REVERT: C 127 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6467 (t80) REVERT: D 31 ILE cc_start: 0.9014 (mt) cc_final: 0.8789 (mp) REVERT: D 90 ASP cc_start: 0.7097 (t0) cc_final: 0.6622 (t0) REVERT: D 143 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8581 (mt-10) REVERT: D 162 LYS cc_start: 0.8312 (mtmt) cc_final: 0.7714 (mttt) REVERT: E 26 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8805 (mm) REVERT: E 112 ASP cc_start: 0.8185 (m-30) cc_final: 0.7903 (m-30) REVERT: E 162 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7665 (mtpt) REVERT: F 90 ASP cc_start: 0.7228 (t0) cc_final: 0.6642 (t0) REVERT: F 127 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: F 133 GLU cc_start: 0.8645 (pm20) cc_final: 0.8050 (pt0) REVERT: F 144 GLU cc_start: 0.8754 (pt0) cc_final: 0.8517 (pt0) REVERT: G 90 ASP cc_start: 0.7279 (t0) cc_final: 0.6908 (t0) REVERT: G 103 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6327 (m) REVERT: H 63 ASP cc_start: 0.8350 (t0) cc_final: 0.8086 (t0) REVERT: H 73 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8547 (mt-10) REVERT: I 59 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7875 (p0) REVERT: I 61 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7884 (mp0) REVERT: I 90 ASP cc_start: 0.7398 (t0) cc_final: 0.6930 (t0) REVERT: J 31 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8563 (mp) REVERT: J 44 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8703 (mt) REVERT: J 73 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8636 (mt-10) REVERT: K 96 TYR cc_start: 0.7393 (t80) cc_final: 0.6709 (t80) REVERT: K 127 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6254 (t80) REVERT: L 31 ILE cc_start: 0.9066 (mp) cc_final: 0.8851 (mp) REVERT: L 61 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7087 (pp20) REVERT: L 133 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: M 94 THR cc_start: 0.6529 (OUTLIER) cc_final: 0.6198 (m) REVERT: M 108 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8870 (mt) REVERT: N 26 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8725 (mm) REVERT: N 90 ASP cc_start: 0.6118 (t70) cc_final: 0.5843 (t70) REVERT: N 93 GLN cc_start: 0.6930 (mt0) cc_final: 0.6675 (pt0) REVERT: N 96 TYR cc_start: 0.7368 (t80) cc_final: 0.7081 (t80) REVERT: O 61 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: O 77 MET cc_start: 0.8891 (mmm) cc_final: 0.8679 (tpt) REVERT: P 127 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.5638 (t80) REVERT: S 94 THR cc_start: 0.6795 (OUTLIER) cc_final: 0.6375 (m) REVERT: S 133 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8026 (mp0) outliers start: 142 outliers final: 75 residues processed: 597 average time/residue: 0.6159 time to fit residues: 416.6889 Evaluate side-chains 607 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 512 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 135 THR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 116 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 196 optimal weight: 0.6980 chunk 120 optimal weight: 0.0030 chunk 204 optimal weight: 0.5980 chunk 42 optimal weight: 0.0000 chunk 40 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121905 restraints weight = 28188.602| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.40 r_work: 0.3243 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20960 Z= 0.118 Angle : 0.695 22.372 28580 Z= 0.322 Chirality : 0.048 0.173 3660 Planarity : 0.002 0.025 3760 Dihedral : 5.454 57.763 3048 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 5.13 % Allowed : 22.24 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 2900 helix: 1.64 (0.21), residues: 520 sheet: 0.24 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 148 TYR 0.005 0.001 TYR J 156 PHE 0.007 0.001 PHE T 42 HIS 0.004 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00264 (20960) covalent geometry : angle 0.69505 (28580) hydrogen bonds : bond 0.04153 ( 860) hydrogen bonds : angle 4.47444 ( 2340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 524 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 73 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8552 (mt-10) REVERT: A 90 ASP cc_start: 0.6955 (t0) cc_final: 0.6722 (t0) REVERT: A 126 ASN cc_start: 0.6337 (p0) cc_final: 0.6060 (p0) REVERT: A 127 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6254 (t80) REVERT: A 143 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8547 (mt-10) REVERT: B 90 ASP cc_start: 0.6838 (t0) cc_final: 0.6585 (t0) REVERT: B 103 THR cc_start: 0.5910 (OUTLIER) cc_final: 0.5294 (p) REVERT: C 61 GLU cc_start: 0.7616 (pp20) cc_final: 0.7328 (pp20) REVERT: C 90 ASP cc_start: 0.6787 (t0) cc_final: 0.6462 (t0) REVERT: C 93 GLN cc_start: 0.6132 (tm130) cc_final: 0.5738 (tm-30) REVERT: C 127 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6472 (t80) REVERT: D 31 ILE cc_start: 0.9023 (mt) cc_final: 0.8798 (mp) REVERT: D 143 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 162 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7759 (mttt) REVERT: E 26 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8643 (mt) REVERT: E 103 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6413 (m) REVERT: E 162 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7775 (mtpt) REVERT: F 90 ASP cc_start: 0.7014 (t0) cc_final: 0.6527 (t0) REVERT: F 127 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: F 133 GLU cc_start: 0.8647 (pm20) cc_final: 0.8117 (pt0) REVERT: F 144 GLU cc_start: 0.8761 (pt0) cc_final: 0.8537 (pt0) REVERT: G 90 ASP cc_start: 0.7327 (t0) cc_final: 0.7075 (t0) REVERT: G 103 THR cc_start: 0.6642 (OUTLIER) cc_final: 0.6243 (m) REVERT: H 63 ASP cc_start: 0.8408 (t0) cc_final: 0.8172 (t0) REVERT: H 73 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8516 (mt-10) REVERT: I 59 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8014 (p0) REVERT: I 61 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7791 (mp0) REVERT: I 90 ASP cc_start: 0.7274 (t0) cc_final: 0.6980 (t0) REVERT: I 126 ASN cc_start: 0.5350 (p0) cc_final: 0.4703 (p0) REVERT: J 31 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8622 (mp) REVERT: J 44 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8742 (mt) REVERT: J 73 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8555 (mt-10) REVERT: K 64 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: K 96 TYR cc_start: 0.7333 (t80) cc_final: 0.6666 (t80) REVERT: K 127 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6291 (t80) REVERT: L 31 ILE cc_start: 0.9092 (mp) cc_final: 0.8837 (mp) REVERT: L 61 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7015 (pp20) REVERT: L 133 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: M 94 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6369 (m) REVERT: M 108 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8915 (mt) REVERT: N 26 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8689 (mm) REVERT: N 96 TYR cc_start: 0.7414 (t80) cc_final: 0.7013 (t80) REVERT: O 61 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7969 (mm-30) REVERT: O 77 MET cc_start: 0.8874 (mmm) cc_final: 0.8658 (tpt) REVERT: P 61 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: R 39 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8331 (mt) REVERT: S 94 THR cc_start: 0.6736 (OUTLIER) cc_final: 0.6309 (m) REVERT: S 133 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: T 42 PHE cc_start: 0.9109 (t80) cc_final: 0.8829 (t80) REVERT: T 116 ILE cc_start: 0.8606 (mt) cc_final: 0.8312 (tt) outliers start: 119 outliers final: 73 residues processed: 575 average time/residue: 0.6033 time to fit residues: 393.5835 Evaluate side-chains 599 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 504 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 135 THR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 179 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119589 restraints weight = 28401.833| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.39 r_work: 0.3206 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20960 Z= 0.145 Angle : 0.740 23.578 28580 Z= 0.337 Chirality : 0.049 0.158 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.412 57.845 3040 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.78 % Allowed : 23.32 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 2900 helix: 1.61 (0.21), residues: 520 sheet: 0.24 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.006 0.001 TYR J 156 PHE 0.007 0.001 PHE T 42 HIS 0.004 0.002 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00345 (20960) covalent geometry : angle 0.73958 (28580) hydrogen bonds : bond 0.04651 ( 860) hydrogen bonds : angle 4.53200 ( 2340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 518 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8942 (mp) REVERT: A 73 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8559 (mt-10) REVERT: A 127 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6138 (t80) REVERT: A 143 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 148 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8639 (mtm180) REVERT: B 90 ASP cc_start: 0.6827 (t0) cc_final: 0.6621 (t0) REVERT: B 103 THR cc_start: 0.5852 (OUTLIER) cc_final: 0.5242 (p) REVERT: C 61 GLU cc_start: 0.7714 (pp20) cc_final: 0.7433 (pp20) REVERT: C 90 ASP cc_start: 0.6830 (t0) cc_final: 0.6428 (t0) REVERT: C 93 GLN cc_start: 0.6135 (tm130) cc_final: 0.5755 (tm-30) REVERT: C 127 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6534 (t80) REVERT: D 31 ILE cc_start: 0.9058 (mt) cc_final: 0.8830 (mp) REVERT: D 143 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8522 (mt-10) REVERT: D 162 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7719 (mttt) REVERT: E 26 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (mm) REVERT: E 103 THR cc_start: 0.6390 (OUTLIER) cc_final: 0.6093 (m) REVERT: E 112 ASP cc_start: 0.8228 (m-30) cc_final: 0.7946 (m-30) REVERT: E 162 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7793 (mtpt) REVERT: F 90 ASP cc_start: 0.7011 (t0) cc_final: 0.6665 (t0) REVERT: F 127 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: F 133 GLU cc_start: 0.8652 (pm20) cc_final: 0.8108 (pt0) REVERT: F 144 GLU cc_start: 0.8803 (pt0) cc_final: 0.8573 (pt0) REVERT: G 90 ASP cc_start: 0.7337 (t0) cc_final: 0.6999 (t0) REVERT: G 103 THR cc_start: 0.6660 (OUTLIER) cc_final: 0.6237 (m) REVERT: H 63 ASP cc_start: 0.8372 (t0) cc_final: 0.8109 (t0) REVERT: H 73 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8532 (mt-10) REVERT: H 90 ASP cc_start: 0.6404 (t0) cc_final: 0.5813 (p0) REVERT: I 59 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8078 (p0) REVERT: I 61 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7772 (mp0) REVERT: I 127 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6276 (t80) REVERT: J 31 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8602 (mp) REVERT: J 44 LEU cc_start: 0.9048 (mp) cc_final: 0.8816 (mt) REVERT: J 73 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8523 (mt-10) REVERT: K 64 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: K 96 TYR cc_start: 0.7384 (t80) cc_final: 0.6783 (t80) REVERT: K 127 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6296 (t80) REVERT: L 61 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: L 133 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: M 94 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6356 (m) REVERT: M 108 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8889 (mt) REVERT: N 26 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8729 (mm) REVERT: N 96 TYR cc_start: 0.7522 (t80) cc_final: 0.7175 (t80) REVERT: O 31 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8391 (mp) REVERT: O 61 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8106 (mm-30) REVERT: P 61 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (mm-30) REVERT: P 127 TYR cc_start: 0.7430 (m-80) cc_final: 0.5770 (t80) REVERT: R 39 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8368 (mt) REVERT: S 89 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7562 (pp) REVERT: S 133 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: T 42 PHE cc_start: 0.9106 (t80) cc_final: 0.8803 (t80) REVERT: T 116 ILE cc_start: 0.8745 (mt) cc_final: 0.8321 (tt) outliers start: 111 outliers final: 76 residues processed: 565 average time/residue: 0.6431 time to fit residues: 410.6173 Evaluate side-chains 609 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 510 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 127 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 147 THR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 135 THR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 108 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 258 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.0060 chunk 180 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN N 126 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119655 restraints weight = 28345.355| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.39 r_work: 0.3208 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20960 Z= 0.143 Angle : 0.748 24.262 28580 Z= 0.339 Chirality : 0.049 0.166 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.376 57.940 3038 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 5.00 % Allowed : 23.10 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 2900 helix: 1.62 (0.21), residues: 520 sheet: 0.24 (0.18), residues: 960 loop : -2.82 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.007 0.001 TYR F 96 PHE 0.007 0.001 PHE T 42 HIS 0.004 0.002 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00340 (20960) covalent geometry : angle 0.74779 (28580) hydrogen bonds : bond 0.04640 ( 860) hydrogen bonds : angle 4.56288 ( 2340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8049.93 seconds wall clock time: 137 minutes 38.39 seconds (8258.39 seconds total)