Starting phenix.real_space_refine on Tue May 20 21:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi2_40060/05_2025/8gi2_40060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi2_40060/05_2025/8gi2_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_40060/05_2025/8gi2_40060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi2_40060/05_2025/8gi2_40060.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi2_40060/05_2025/8gi2_40060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi2_40060/05_2025/8gi2_40060.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 5.05, per 1000 atoms: 0.24 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: 5.82 Conformation dependent library (CDL) restraints added in 3.1 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: 2.13 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: 5.66 Time building geometry restraints manager: 6.69 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: 0.23 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain '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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 39.170 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS E 82 PHE 0.003 0.001 PHE P 159 TYR 0.007 0.001 TYR H 127 ARG 0.001 0.000 ARG J 148 Details of bonding type rmsd hydrogen bonds : bond 0.16360 ( 860) hydrogen bonds : angle 5.06380 ( 2340) covalent geometry : bond 0.00758 (20960) covalent geometry : angle 0.97532 (28580) *********************** 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 : 2.159 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: 0.7979 (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: 0.5738 (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: 0.4274 (t80) outliers start: 80 outliers final: 44 residues processed: 706 average time/residue: 1.0744 time to fit residues: 879.9913 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 : 2.220 ------------------------------------------------------------------------------- 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 236 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 C 126 ASN E 59 ASN I 126 ASN J 126 ASN L 55 GLN L 126 ASN M 82 HIS M 126 ASN N 126 ASN O 69 ASN P 69 ASN P 126 ASN Q 69 ASN R 69 ASN R 126 ASN T 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118621 restraints weight = 28048.746| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.33 r_work: 0.3315 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20960 Z= 0.122 Angle : 0.642 12.701 28580 Z= 0.328 Chirality : 0.048 0.145 3660 Planarity : 0.003 0.021 3760 Dihedral : 6.797 78.654 3120 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 6.47 % Allowed : 14.40 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.15), residues: 2900 helix: 0.37 (0.23), residues: 560 sheet: -0.26 (0.18), residues: 960 loop : -3.73 (0.11), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 82 PHE 0.019 0.001 PHE T 42 TYR 0.007 0.001 TYR F 127 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 860) hydrogen bonds : angle 4.65556 ( 2340) covalent geometry : bond 0.00258 (20960) covalent geometry : angle 0.64204 (28580) *********************** 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 722 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 572 time to evaluate : 2.155 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: A 73 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8579 (mt-10) REVERT: A 143 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 61 GLU cc_start: 0.7575 (pp20) cc_final: 0.7343 (pp20) REVERT: C 90 ASP cc_start: 0.6818 (t0) cc_final: 0.6579 (t0) REVERT: C 127 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6080 (t80) REVERT: C 133 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 31 ILE cc_start: 0.9068 (mt) cc_final: 0.8769 (mp) REVERT: D 143 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 162 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7693 (mtpt) REVERT: F 64 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (mt-10) REVERT: F 143 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8485 (mt-10) REVERT: G 90 ASP cc_start: 0.6862 (t0) cc_final: 0.6614 (t0) REVERT: H 63 ASP cc_start: 0.8464 (t0) cc_final: 0.8204 (t0) REVERT: H 73 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8663 (mt-10) REVERT: H 112 ASP cc_start: 0.8318 (m-30) cc_final: 0.7891 (m-30) REVERT: I 90 ASP cc_start: 0.7135 (t0) cc_final: 0.6797 (t0) REVERT: J 44 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8610 (mt) REVERT: J 73 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8579 (mt-10) REVERT: K 127 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6192 (t80) REVERT: L 133 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7824 (mp0) REVERT: M 73 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8772 (mt-10) REVERT: M 108 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8863 (mt) REVERT: N 81 ASP cc_start: 0.8719 (m-30) cc_final: 0.8326 (m-30) REVERT: N 127 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6098 (t80) REVERT: O 90 ASP cc_start: 0.6250 (t0) cc_final: 0.6034 (t0) REVERT: O 96 TYR cc_start: 0.7509 (t80) cc_final: 0.6999 (t80) REVERT: O 127 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6062 (t80) REVERT: R 63 ASP cc_start: 0.8640 (t0) cc_final: 0.8331 (t0) REVERT: R 127 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.5756 (t80) REVERT: S 94 THR cc_start: 0.6830 (t) cc_final: 0.6456 (m) REVERT: S 127 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.5929 (t80) REVERT: T 46 LEU cc_start: 0.8753 (tp) cc_final: 0.8539 (tt) REVERT: T 123 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.7566 (t) REVERT: T 146 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8253 (mm-30) outliers start: 150 outliers final: 62 residues processed: 629 average time/residue: 1.1533 time to fit residues: 829.7641 Evaluate side-chains 608 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 536 time to evaluate : 2.253 ------------------------------------------------------------------------------- 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 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 127 TYR 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 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE 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 127 TYR Chi-restraints excluded: chain J residue 19 VAL 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 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 L residue 26 ILE 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 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 22 VAL 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 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 94 THR Chi-restraints excluded: chain R residue 127 TYR 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 T residue 23 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 123 SER Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 79 optimal weight: 8.9990 chunk 159 optimal weight: 0.0970 chunk 244 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 273 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN D 82 HIS E 59 ASN K 126 ASN L 55 GLN L 93 GLN N 82 HIS N 119 ASN O 119 ASN P 119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111426 restraints weight = 28217.162| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.28 r_work: 0.3214 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20960 Z= 0.201 Angle : 0.696 16.079 28580 Z= 0.347 Chirality : 0.050 0.168 3660 Planarity : 0.003 0.026 3760 Dihedral : 6.485 54.405 3060 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 7.84 % Allowed : 14.96 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2900 helix: 0.63 (0.22), residues: 580 sheet: -0.12 (0.18), residues: 960 loop : -3.30 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS P 82 PHE 0.013 0.002 PHE J 42 TYR 0.009 0.001 TYR F 127 ARG 0.002 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 860) hydrogen bonds : angle 4.84515 ( 2340) covalent geometry : bond 0.00488 (20960) covalent geometry : angle 0.69608 (28580) *********************** 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 744 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 562 time to evaluate : 2.198 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: 0.8860 (mt-10) cc_final: 0.8592 (mt-10) REVERT: A 90 ASP cc_start: 0.6553 (t0) cc_final: 0.6304 (t0) REVERT: A 127 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 143 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 103 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.5890 (p) REVERT: B 144 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: C 26 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 61 GLU cc_start: 0.7800 (pp20) cc_final: 0.7571 (pp20) REVERT: C 90 ASP cc_start: 0.7098 (t0) cc_final: 0.6664 (t0) REVERT: C 127 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.6368 (t80) REVERT: C 133 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 31 ILE cc_start: 0.9093 (mt) cc_final: 0.8801 (mp) REVERT: D 90 ASP cc_start: 0.6997 (t0) cc_final: 0.6690 (t0) REVERT: D 127 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6353 (t80) REVERT: D 143 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8585 (mt-10) REVERT: E 26 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (mm) REVERT: E 112 ASP cc_start: 0.8269 (m-30) cc_final: 0.8006 (m-30) REVERT: E 162 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7702 (mtpt) REVERT: F 90 ASP cc_start: 0.7315 (t0) cc_final: 0.7085 (t0) REVERT: F 133 GLU cc_start: 0.8649 (pm20) cc_final: 0.8178 (pt0) REVERT: G 90 ASP cc_start: 0.6889 (t0) cc_final: 0.6482 (t0) REVERT: H 73 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8578 (mt-10) REVERT: I 90 ASP cc_start: 0.7285 (t0) cc_final: 0.6831 (t0) REVERT: J 73 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8640 (mt-10) REVERT: J 133 GLU cc_start: 0.8721 (pt0) cc_final: 0.8454 (pt0) REVERT: K 127 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6301 (t80) REVERT: L 144 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: M 108 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8959 (mt) REVERT: N 81 ASP cc_start: 0.8671 (m-30) cc_final: 0.8325 (m-30) REVERT: N 96 TYR cc_start: 0.7683 (t80) cc_final: 0.7229 (t80) REVERT: N 127 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6369 (t80) REVERT: N 143 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8679 (mt-10) REVERT: O 26 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.9042 (mm) REVERT: O 90 ASP cc_start: 0.6602 (t0) cc_final: 0.6228 (t0) REVERT: O 108 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8931 (mp) REVERT: O 127 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.6252 (t80) REVERT: P 61 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: R 127 TYR cc_start: 0.7462 (OUTLIER) cc_final: 0.6061 (t80) REVERT: S 46 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8646 (tp) REVERT: S 60 MET cc_start: 0.8902 (mtp) cc_final: 0.8675 (mtp) REVERT: S 90 ASP cc_start: 0.5715 (t0) cc_final: 0.5292 (t0) REVERT: S 133 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: T 90 ASP cc_start: 0.5992 (t0) cc_final: 0.5780 (t0) REVERT: T 101 LYS cc_start: 0.7904 (mmtm) cc_final: 0.7578 (mmtm) outliers start: 182 outliers final: 82 residues processed: 630 average time/residue: 1.2139 time to fit residues: 870.3848 Evaluate side-chains 637 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 537 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 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 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 144 GLU 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 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 50 VAL 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 50 VAL Chi-restraints excluded: chain F residue 94 THR 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 44 LEU Chi-restraints excluded: chain H residue 94 THR 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 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 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 L residue 144 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 MET 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 26 ILE Chi-restraints excluded: chain O residue 50 VAL 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 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 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER 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 127 TYR Chi-restraints excluded: chain R residue 144 GLU 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 127 TYR 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 103 THR 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 31 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 279 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 0.0970 chunk 182 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN E 52 ASN E 59 ASN G 52 ASN L 55 GLN N 119 ASN Q 93 GLN Q 126 ASN S 93 GLN S 126 ASN T 119 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119821 restraints weight = 28367.681| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.31 r_work: 0.3314 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20960 Z= 0.108 Angle : 0.626 16.094 28580 Z= 0.306 Chirality : 0.047 0.145 3660 Planarity : 0.002 0.025 3760 Dihedral : 5.875 54.883 3056 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 6.64 % Allowed : 18.15 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2900 helix: 1.14 (0.22), residues: 560 sheet: 0.27 (0.19), residues: 940 loop : -3.04 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 82 PHE 0.009 0.001 PHE P 42 TYR 0.005 0.001 TYR N 156 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 860) hydrogen bonds : angle 4.52415 ( 2340) covalent geometry : bond 0.00227 (20960) covalent geometry : angle 0.62581 (28580) *********************** 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 704 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 550 time to evaluate : 2.279 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: A 73 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8543 (mt-10) REVERT: A 127 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6379 (t80) REVERT: A 143 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8517 (mt-10) REVERT: B 103 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.5669 (p) REVERT: C 61 GLU cc_start: 0.7604 (pp20) cc_final: 0.7403 (pp20) REVERT: C 90 ASP cc_start: 0.7038 (t0) cc_final: 0.6653 (t0) REVERT: C 127 TYR cc_start: 0.7500 (OUTLIER) cc_final: 0.6090 (t80) REVERT: D 31 ILE cc_start: 0.9038 (mt) cc_final: 0.8775 (mp) REVERT: D 143 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8554 (mt-10) REVERT: E 26 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8845 (mm) REVERT: E 90 ASP cc_start: 0.6359 (t0) cc_final: 0.6120 (p0) REVERT: E 162 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7643 (mtpt) REVERT: F 90 ASP cc_start: 0.7519 (t0) cc_final: 0.7282 (t0) REVERT: F 133 GLU cc_start: 0.8669 (pm20) cc_final: 0.8225 (pt0) REVERT: G 90 ASP cc_start: 0.7106 (t0) cc_final: 0.6844 (t0) REVERT: G 103 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6645 (m) REVERT: H 63 ASP cc_start: 0.8423 (t0) cc_final: 0.8175 (t0) REVERT: H 73 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8594 (mt-10) REVERT: I 44 LEU cc_start: 0.9082 (mt) cc_final: 0.8879 (mt) REVERT: I 90 ASP cc_start: 0.7293 (t0) cc_final: 0.6985 (t0) REVERT: J 44 LEU cc_start: 0.8981 (mp) cc_final: 0.8692 (mt) REVERT: J 73 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8725 (mt-10) REVERT: J 127 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6093 (t80) REVERT: J 133 GLU cc_start: 0.8674 (pt0) cc_final: 0.8454 (pt0) REVERT: K 96 TYR cc_start: 0.7196 (t80) cc_final: 0.6673 (t80) REVERT: K 127 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6369 (t80) REVERT: L 90 ASP cc_start: 0.6767 (t0) cc_final: 0.6403 (t0) REVERT: L 133 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7784 (mp0) REVERT: M 108 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8920 (mt) REVERT: N 53 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7392 (mm-30) REVERT: N 96 TYR cc_start: 0.7521 (t80) cc_final: 0.6783 (t80) REVERT: N 127 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6247 (t80) REVERT: O 31 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8730 (mp) REVERT: O 61 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8119 (mm-30) REVERT: O 127 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.5914 (t80) REVERT: P 61 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7993 (mm-30) REVERT: R 46 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8723 (tt) REVERT: S 60 MET cc_start: 0.8782 (mtp) cc_final: 0.8553 (mtp) REVERT: S 90 ASP cc_start: 0.5638 (t0) cc_final: 0.5405 (t0) REVERT: S 133 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: T 90 ASP cc_start: 0.5981 (t0) cc_final: 0.5763 (t0) REVERT: T 101 LYS cc_start: 0.7820 (mmtm) cc_final: 0.7606 (mmtm) outliers start: 154 outliers final: 64 residues processed: 609 average time/residue: 1.1880 time to fit residues: 824.0702 Evaluate side-chains 599 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 522 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE 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 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 127 TYR 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 94 THR Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 46 LEU 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 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 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 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 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 31 ILE 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 50 VAL 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 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 T residue 50 VAL Chi-restraints excluded: chain T residue 119 ASN 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 212 optimal weight: 0.6980 chunk 231 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 198 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 55 GLN L 93 GLN ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116992 restraints weight = 28308.158| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.30 r_work: 0.3293 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20960 Z= 0.137 Angle : 0.656 20.315 28580 Z= 0.315 Chirality : 0.048 0.156 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.918 54.228 3056 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 7.20 % Allowed : 18.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 2900 helix: 1.13 (0.21), residues: 580 sheet: 0.13 (0.18), residues: 960 loop : -2.85 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS P 82 PHE 0.007 0.001 PHE P 42 TYR 0.006 0.001 TYR F 127 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 860) hydrogen bonds : angle 4.58877 ( 2340) covalent geometry : bond 0.00319 (20960) covalent geometry : angle 0.65567 (28580) *********************** 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 705 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 538 time to evaluate : 2.244 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 31 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9024 (mp) REVERT: A 73 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 90 ASP cc_start: 0.6769 (t0) cc_final: 0.6538 (t0) REVERT: A 126 ASN cc_start: 0.5692 (p0) cc_final: 0.5427 (p0) REVERT: A 127 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6361 (t80) REVERT: A 143 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8570 (mt-10) REVERT: B 103 THR cc_start: 0.6306 (OUTLIER) cc_final: 0.5695 (p) REVERT: C 61 GLU cc_start: 0.7686 (pp20) cc_final: 0.7449 (pp20) REVERT: C 90 ASP cc_start: 0.7082 (t0) cc_final: 0.6686 (t0) REVERT: C 127 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6172 (t80) REVERT: D 31 ILE cc_start: 0.9097 (mt) cc_final: 0.8859 (mp) REVERT: D 127 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.6219 (t80) REVERT: D 143 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8580 (mt-10) REVERT: E 26 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8885 (mm) REVERT: E 162 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7696 (mtpt) REVERT: F 90 ASP cc_start: 0.7583 (t0) cc_final: 0.7320 (t0) REVERT: F 133 GLU cc_start: 0.8685 (pm20) cc_final: 0.8216 (pt0) REVERT: G 90 ASP cc_start: 0.7150 (t0) cc_final: 0.6811 (t0) REVERT: G 103 THR cc_start: 0.6600 (OUTLIER) cc_final: 0.6286 (m) REVERT: H 63 ASP cc_start: 0.8443 (t0) cc_final: 0.8203 (t0) REVERT: H 73 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8589 (mt-10) REVERT: H 90 ASP cc_start: 0.6575 (t0) cc_final: 0.6238 (t0) REVERT: I 90 ASP cc_start: 0.7175 (t0) cc_final: 0.6673 (t0) REVERT: J 31 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8641 (mp) REVERT: J 44 LEU cc_start: 0.9096 (mp) cc_final: 0.8857 (mt) REVERT: J 73 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8718 (mt-10) REVERT: J 127 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6275 (t80) REVERT: J 133 GLU cc_start: 0.8658 (pt0) cc_final: 0.8441 (pt0) REVERT: K 127 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6410 (t80) REVERT: L 133 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: L 144 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: M 108 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8935 (mt) REVERT: N 96 TYR cc_start: 0.7540 (t80) cc_final: 0.6890 (t80) REVERT: N 127 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6303 (t80) REVERT: O 61 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8126 (mm-30) REVERT: O 127 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6112 (t80) REVERT: P 53 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7453 (mm-30) REVERT: P 96 TYR cc_start: 0.7269 (t80) cc_final: 0.6666 (t80) REVERT: P 127 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6095 (t80) REVERT: Q 89 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (mp) REVERT: T 90 ASP cc_start: 0.6065 (t0) cc_final: 0.5818 (t0) outliers start: 167 outliers final: 80 residues processed: 604 average time/residue: 1.2195 time to fit residues: 837.8178 Evaluate side-chains 620 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 523 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 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 A residue 133 GLU Chi-restraints excluded: chain A residue 144 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 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 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 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 26 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 45 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 I residue 154 VAL Chi-restraints excluded: chain J residue 31 ILE 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 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 105 LYS 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 60 MET 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 39 ILE Chi-restraints excluded: chain O residue 50 VAL 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 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 103 THR Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER 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 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 127 TYR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 56 optimal weight: 0.9980 chunk 259 optimal weight: 0.0270 chunk 21 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 50 optimal weight: 0.0040 overall best weight: 0.9452 ------------------------------------------------------------------------------- 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** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN O 126 ASN R 126 ASN ** S 93 GLN ** 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 = 0.3683 r_free = 0.3683 target = 0.148902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122042 restraints weight = 28444.798| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.39 r_work: 0.3240 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20960 Z= 0.115 Angle : 0.653 20.279 28580 Z= 0.311 Chirality : 0.047 0.147 3660 Planarity : 0.002 0.028 3760 Dihedral : 5.726 55.749 3056 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 6.68 % Allowed : 19.96 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2900 helix: 1.45 (0.21), residues: 560 sheet: 0.21 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.007 0.001 PHE P 42 TYR 0.006 0.001 TYR F 127 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 860) hydrogen bonds : angle 4.48942 ( 2340) covalent geometry : bond 0.00254 (20960) covalent geometry : angle 0.65322 (28580) *********************** 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 679 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 524 time to evaluate : 2.310 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 31 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 73 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8562 (mt-10) REVERT: A 127 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6198 (t80) REVERT: A 143 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 103 THR cc_start: 0.6148 (OUTLIER) cc_final: 0.5581 (p) REVERT: C 61 GLU cc_start: 0.7537 (pp20) cc_final: 0.7238 (pp20) REVERT: C 90 ASP cc_start: 0.6876 (t0) cc_final: 0.6536 (t0) REVERT: C 93 GLN cc_start: 0.5642 (tm130) cc_final: 0.5299 (tm-30) REVERT: C 127 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6367 (t80) REVERT: D 31 ILE cc_start: 0.9047 (mt) cc_final: 0.8827 (mp) REVERT: D 143 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 26 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8751 (mm) REVERT: E 90 ASP cc_start: 0.6164 (t0) cc_final: 0.5785 (p0) REVERT: E 103 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6299 (m) REVERT: E 162 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7739 (mtpt) REVERT: F 127 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6651 (m-80) REVERT: F 133 GLU cc_start: 0.8644 (pm20) cc_final: 0.8047 (pt0) REVERT: F 144 GLU cc_start: 0.8813 (tt0) cc_final: 0.8593 (pt0) REVERT: G 90 ASP cc_start: 0.7205 (t0) cc_final: 0.6818 (t0) REVERT: H 63 ASP cc_start: 0.8276 (t0) cc_final: 0.8029 (t0) REVERT: H 73 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8530 (mt-10) REVERT: H 90 ASP cc_start: 0.6516 (t0) cc_final: 0.6285 (t0) REVERT: I 59 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.7903 (p0) REVERT: I 90 ASP cc_start: 0.7235 (t0) cc_final: 0.6844 (t0) REVERT: J 31 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8587 (mp) REVERT: J 73 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8681 (mt-10) REVERT: J 133 GLU cc_start: 0.8682 (pt0) cc_final: 0.8449 (pt0) REVERT: K 96 TYR cc_start: 0.7180 (t80) cc_final: 0.6623 (t80) REVERT: K 127 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6291 (t80) REVERT: L 31 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8855 (mp) REVERT: L 133 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: M 94 THR cc_start: 0.6528 (OUTLIER) cc_final: 0.6241 (m) REVERT: M 108 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8894 (mt) REVERT: N 26 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8834 (mm) REVERT: N 96 TYR cc_start: 0.7482 (t80) cc_final: 0.6778 (t80) REVERT: N 127 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6188 (t80) REVERT: O 61 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7888 (mm-30) REVERT: O 90 ASP cc_start: 0.6137 (t0) cc_final: 0.5920 (t0) REVERT: O 127 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.5928 (t80) REVERT: P 53 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7246 (mm-30) REVERT: P 127 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5847 (t80) REVERT: Q 89 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.8099 (mp) REVERT: S 133 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: T 90 ASP cc_start: 0.6080 (t0) cc_final: 0.5800 (t0) outliers start: 155 outliers final: 71 residues processed: 590 average time/residue: 1.1801 time to fit residues: 796.1049 Evaluate side-chains 592 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 501 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 126 ASN 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 26 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR 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 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 50 VAL 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 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 127 TYR 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 45 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 I residue 154 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP 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 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 31 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 94 THR 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 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 M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE 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 39 ILE Chi-restraints excluded: chain O residue 50 VAL 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 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 103 THR 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 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 49 optimal weight: 6.9990 chunk 86 optimal weight: 0.0370 chunk 225 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 6 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 219 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 55 GLN ** S 93 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124333 restraints weight = 28298.049| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.40 r_work: 0.3265 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20960 Z= 0.107 Angle : 0.661 21.026 28580 Z= 0.309 Chirality : 0.047 0.153 3660 Planarity : 0.002 0.025 3760 Dihedral : 5.372 56.257 3050 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.82 % Allowed : 20.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2900 helix: 1.63 (0.21), residues: 520 sheet: 0.47 (0.18), residues: 940 loop : -2.78 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.007 0.001 PHE P 42 TYR 0.005 0.001 TYR N 156 ARG 0.000 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 860) hydrogen bonds : angle 4.39591 ( 2340) covalent geometry : bond 0.00229 (20960) covalent geometry : angle 0.66109 (28580) *********************** 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 650 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 515 time to evaluate : 2.166 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: A 31 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8845 (mp) REVERT: A 73 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8497 (mt-10) REVERT: A 90 ASP cc_start: 0.6203 (t0) cc_final: 0.5776 (p0) REVERT: A 126 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5545 (p0) REVERT: A 143 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8467 (mt-10) REVERT: B 103 THR cc_start: 0.5892 (OUTLIER) cc_final: 0.5261 (p) REVERT: C 61 GLU cc_start: 0.7557 (pp20) cc_final: 0.7340 (pp20) REVERT: C 90 ASP cc_start: 0.6774 (t0) cc_final: 0.6524 (t0) REVERT: C 93 GLN cc_start: 0.5607 (tm130) cc_final: 0.5278 (tm-30) REVERT: C 127 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6317 (t80) REVERT: D 31 ILE cc_start: 0.9020 (mt) cc_final: 0.8805 (mp) REVERT: D 143 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8506 (mt-10) REVERT: E 26 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8642 (mt) REVERT: E 103 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6298 (m) REVERT: E 162 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7775 (mtpt) REVERT: F 127 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: F 133 GLU cc_start: 0.8597 (pm20) cc_final: 0.8014 (pt0) REVERT: F 155 ASP cc_start: 0.8630 (m-30) cc_final: 0.8422 (m-30) REVERT: G 90 ASP cc_start: 0.7120 (t0) cc_final: 0.6770 (t0) REVERT: H 59 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8232 (p0) REVERT: H 61 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: H 63 ASP cc_start: 0.8327 (t0) cc_final: 0.8113 (t0) REVERT: H 73 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8492 (mt-10) REVERT: I 90 ASP cc_start: 0.7269 (t0) cc_final: 0.6901 (t0) REVERT: J 31 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8681 (mp) REVERT: J 73 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8654 (mt-10) REVERT: J 133 GLU cc_start: 0.8664 (pt0) cc_final: 0.8435 (pt0) REVERT: K 96 TYR cc_start: 0.7223 (t80) cc_final: 0.6676 (t80) REVERT: K 127 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6426 (t80) REVERT: L 31 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8793 (mp) REVERT: L 133 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: M 94 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6316 (m) REVERT: M 108 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8913 (mt) REVERT: N 26 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8739 (mm) REVERT: N 96 TYR cc_start: 0.7520 (t80) cc_final: 0.6695 (t80) REVERT: N 127 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6258 (t80) REVERT: O 61 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7815 (mm-30) REVERT: P 53 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7148 (mm-30) REVERT: P 96 TYR cc_start: 0.7110 (t80) cc_final: 0.6292 (t80) REVERT: P 127 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.5986 (t80) REVERT: S 39 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8675 (mt) REVERT: S 133 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: T 42 PHE cc_start: 0.9068 (t80) cc_final: 0.8697 (t80) REVERT: T 90 ASP cc_start: 0.5911 (t0) cc_final: 0.5671 (t0) outliers start: 135 outliers final: 72 residues processed: 579 average time/residue: 1.1542 time to fit residues: 763.0177 Evaluate side-chains 591 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 499 time to evaluate : 2.173 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 126 ASN 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 26 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 133 GLU 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 64 GLU 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 127 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain H residue 61 GLU 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 I residue 45 ASP 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 I residue 154 VAL 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 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL 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 31 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 133 GLU 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 M residue 155 ASP 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 O residue 50 VAL 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 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 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 39 ILE 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 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR 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 36 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 chunk 89 optimal weight: 10.0000 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 59 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN N 119 ASN ** S 93 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118662 restraints weight = 28568.446| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.37 r_work: 0.3200 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20960 Z= 0.157 Angle : 0.710 21.989 28580 Z= 0.333 Chirality : 0.050 0.162 3660 Planarity : 0.002 0.027 3760 Dihedral : 5.643 55.892 3048 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 6.21 % Allowed : 21.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2900 helix: 1.62 (0.21), residues: 520 sheet: 0.26 (0.18), residues: 960 loop : -2.77 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS P 82 PHE 0.021 0.001 PHE R 42 TYR 0.005 0.001 TYR J 156 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 860) hydrogen bonds : angle 4.56644 ( 2340) covalent geometry : bond 0.00377 (20960) covalent geometry : angle 0.70966 (28580) *********************** 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 663 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 519 time to evaluate : 2.117 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: 0.9186 (OUTLIER) cc_final: 0.8932 (mp) REVERT: A 73 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 143 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8572 (mt-10) REVERT: B 90 ASP cc_start: 0.6843 (t0) cc_final: 0.6535 (t0) REVERT: B 103 THR cc_start: 0.5900 (OUTLIER) cc_final: 0.5243 (p) REVERT: C 61 GLU cc_start: 0.7679 (pp20) cc_final: 0.7385 (pp20) REVERT: C 90 ASP cc_start: 0.6879 (t0) cc_final: 0.6534 (t0) REVERT: C 93 GLN cc_start: 0.6127 (tm130) cc_final: 0.5811 (tm-30) REVERT: C 127 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6468 (t80) REVERT: D 31 ILE cc_start: 0.9068 (mt) cc_final: 0.8844 (mp) REVERT: D 143 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8574 (mt-10) REVERT: E 26 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8799 (mm) REVERT: E 103 THR cc_start: 0.6288 (OUTLIER) cc_final: 0.6002 (m) REVERT: E 112 ASP cc_start: 0.8246 (m-30) cc_final: 0.7926 (m-30) REVERT: E 162 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7678 (mtpt) REVERT: F 133 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: F 144 GLU cc_start: 0.8923 (tt0) cc_final: 0.8695 (pt0) REVERT: G 90 ASP cc_start: 0.7237 (t0) cc_final: 0.6824 (t0) REVERT: G 103 THR cc_start: 0.6383 (OUTLIER) cc_final: 0.6060 (m) REVERT: G 106 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5856 (mm) REVERT: G 144 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: H 63 ASP cc_start: 0.8332 (t0) cc_final: 0.8072 (t0) REVERT: H 73 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8546 (mt-10) REVERT: I 90 ASP cc_start: 0.7231 (t0) cc_final: 0.6905 (t0) REVERT: J 31 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8623 (mp) REVERT: J 73 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8545 (mt-10) REVERT: J 127 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6234 (t80) REVERT: J 133 GLU cc_start: 0.8646 (pt0) cc_final: 0.8429 (pt0) REVERT: K 64 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: K 96 TYR cc_start: 0.7209 (t80) cc_final: 0.6541 (t80) REVERT: K 127 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6122 (t80) REVERT: L 61 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: L 133 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: M 94 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6765 (m) REVERT: M 108 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8938 (mt) REVERT: N 26 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8701 (mm) REVERT: N 96 TYR cc_start: 0.7578 (t80) cc_final: 0.6799 (t80) REVERT: N 127 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6242 (t80) REVERT: O 61 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7976 (mm-30) REVERT: P 53 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7303 (mm-30) REVERT: P 107 LYS cc_start: 0.8838 (mptt) cc_final: 0.8546 (mttm) REVERT: P 127 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.5879 (t80) REVERT: R 28 MET cc_start: 0.9078 (mmp) cc_final: 0.8708 (mmt) REVERT: R 117 ASN cc_start: 0.8445 (t0) cc_final: 0.7614 (t0) REVERT: S 133 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: T 42 PHE cc_start: 0.9084 (t80) cc_final: 0.8764 (t80) REVERT: T 90 ASP cc_start: 0.6104 (t0) cc_final: 0.5759 (t0) outliers start: 144 outliers final: 83 residues processed: 588 average time/residue: 1.1705 time to fit residues: 784.9610 Evaluate side-chains 607 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 503 time to evaluate : 2.388 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 133 GLU 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 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 106 LEU 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 133 GLU 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 106 LEU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU 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 106 LEU 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 45 ASP 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 I residue 154 VAL 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 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 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 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 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 M residue 144 GLU Chi-restraints excluded: chain M residue 155 ASP 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 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 103 THR Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER 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 108 LEU 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 89 ILE Chi-restraints excluded: chain T residue 127 TYR 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 77 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 259 optimal weight: 4.9990 chunk 269 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 59 ASN F 126 ASN H 93 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN O 55 GLN Q 119 ASN ** S 93 GLN ** 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 = 0.3619 r_free = 0.3619 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116527 restraints weight = 28523.566| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.37 r_work: 0.3173 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3546 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= 0.187 Angle : 0.768 23.465 28580 Z= 0.353 Chirality : 0.051 0.169 3660 Planarity : 0.003 0.028 3760 Dihedral : 5.865 56.352 3046 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 5.95 % Allowed : 21.81 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 2900 helix: 1.32 (0.20), residues: 540 sheet: 0.17 (0.18), residues: 960 loop : -2.77 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS P 82 PHE 0.008 0.001 PHE J 42 TYR 0.005 0.001 TYR F 156 ARG 0.002 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 860) hydrogen bonds : angle 4.67658 ( 2340) covalent geometry : bond 0.00457 (20960) covalent geometry : angle 0.76803 (28580) *********************** 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 658 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 520 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9020 (mp) REVERT: A 73 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 103 THR cc_start: 0.5871 (OUTLIER) cc_final: 0.5216 (p) REVERT: C 61 GLU cc_start: 0.7839 (pp20) cc_final: 0.7531 (pp20) REVERT: C 90 ASP cc_start: 0.6961 (t0) cc_final: 0.6523 (t0) REVERT: C 93 GLN cc_start: 0.6319 (tm130) cc_final: 0.5997 (tm-30) REVERT: C 106 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5834 (mm) REVERT: C 127 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6573 (t80) REVERT: D 31 ILE cc_start: 0.9104 (mt) cc_final: 0.8872 (mp) REVERT: D 143 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8573 (mt-10) REVERT: D 162 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7944 (mmmt) REVERT: E 26 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8843 (mm) REVERT: E 112 ASP cc_start: 0.8205 (m-30) cc_final: 0.7891 (m-30) REVERT: E 162 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7740 (mtpt) REVERT: F 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: F 144 GLU cc_start: 0.8916 (tt0) cc_final: 0.8704 (pt0) REVERT: G 90 ASP cc_start: 0.7293 (t0) cc_final: 0.6975 (t0) REVERT: G 103 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6175 (m) REVERT: G 144 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: H 73 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8579 (mt-10) REVERT: I 90 ASP cc_start: 0.7485 (t0) cc_final: 0.7121 (t0) REVERT: I 127 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6522 (t80) REVERT: J 73 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8544 (mt-10) REVERT: J 93 GLN cc_start: 0.5655 (tm130) cc_final: 0.5049 (tm-30) REVERT: J 127 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6297 (t80) REVERT: K 93 GLN cc_start: 0.5042 (tm130) cc_final: 0.4710 (tm-30) REVERT: K 127 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6444 (t80) REVERT: L 53 GLU cc_start: 0.7963 (tp30) cc_final: 0.7738 (tp30) REVERT: L 60 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8471 (mtm) REVERT: L 61 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7465 (pp20) REVERT: L 133 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: L 144 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: M 94 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6780 (m) REVERT: M 108 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8958 (mt) REVERT: N 26 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8758 (mm) REVERT: N 96 TYR cc_start: 0.7645 (t80) cc_final: 0.6854 (t80) REVERT: N 127 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6234 (t80) REVERT: O 61 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8173 (mm-30) REVERT: O 77 MET cc_start: 0.8893 (mmm) cc_final: 0.8597 (tpt) REVERT: P 53 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7423 (mm-30) REVERT: P 96 TYR cc_start: 0.7297 (t80) cc_final: 0.6370 (t80) REVERT: P 107 LYS cc_start: 0.8848 (mptt) cc_final: 0.8541 (mttm) REVERT: P 127 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.5969 (t80) REVERT: R 28 MET cc_start: 0.9223 (mmp) cc_final: 0.8942 (mmt) REVERT: R 117 ASN cc_start: 0.8517 (t0) cc_final: 0.7735 (t0) REVERT: S 39 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8623 (mt) REVERT: T 89 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7298 (mp) REVERT: T 90 ASP cc_start: 0.6201 (t0) cc_final: 0.5849 (t0) outliers start: 138 outliers final: 85 residues processed: 583 average time/residue: 1.2564 time to fit residues: 834.6317 Evaluate side-chains 620 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 513 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 94 THR 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 106 LEU 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 90 ASP 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 50 VAL 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 144 GLU 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 50 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 133 GLU 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 144 GLU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 106 LEU 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 45 ASP 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 I residue 154 VAL Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 60 MET 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 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 60 MET 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 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 M residue 144 GLU Chi-restraints excluded: chain M residue 155 ASP 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 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 103 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER 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 108 LEU Chi-restraints excluded: chain S residue 39 ILE 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 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR 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 233 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 271 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 59 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** 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** Q 119 ASN ** S 93 GLN ** 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 = 0.3660 r_free = 0.3660 target = 0.147024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120224 restraints weight = 28192.823| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.36 r_work: 0.3216 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20960 Z= 0.130 Angle : 0.750 23.852 28580 Z= 0.337 Chirality : 0.049 0.158 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.557 57.200 3044 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.14 % Allowed : 24.22 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2900 helix: 1.62 (0.21), residues: 520 sheet: 0.24 (0.18), residues: 960 loop : -2.78 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.026 0.001 PHE R 42 TYR 0.005 0.001 TYR F 96 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 860) hydrogen bonds : angle 4.57836 ( 2340) covalent geometry : bond 0.00298 (20960) covalent geometry : angle 0.75002 (28580) ********************** 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 616 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 520 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8940 (mp) REVERT: A 73 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8522 (mt-10) REVERT: A 143 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 103 THR cc_start: 0.5782 (OUTLIER) cc_final: 0.5150 (p) REVERT: C 61 GLU cc_start: 0.7624 (pp20) cc_final: 0.7298 (pp20) REVERT: C 90 ASP cc_start: 0.6923 (t0) cc_final: 0.6521 (t0) REVERT: C 93 GLN cc_start: 0.6054 (tm130) cc_final: 0.5780 (tm-30) REVERT: C 106 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6112 (mm) REVERT: C 127 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6406 (t80) REVERT: D 31 ILE cc_start: 0.9045 (mt) cc_final: 0.8820 (mp) REVERT: D 116 ILE cc_start: 0.8904 (mt) cc_final: 0.8692 (mt) REVERT: D 143 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8556 (mt-10) REVERT: D 162 LYS cc_start: 0.8325 (mtmt) cc_final: 0.7670 (mttt) REVERT: E 26 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8794 (mm) REVERT: E 112 ASP cc_start: 0.8217 (m-30) cc_final: 0.7899 (m-30) REVERT: E 162 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7742 (mtpt) REVERT: F 133 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: F 144 GLU cc_start: 0.8824 (tt0) cc_final: 0.8623 (pt0) REVERT: F 155 ASP cc_start: 0.8642 (m-30) cc_final: 0.8430 (m-30) REVERT: G 90 ASP cc_start: 0.7213 (t0) cc_final: 0.6892 (t0) REVERT: G 103 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.6073 (m) REVERT: H 63 ASP cc_start: 0.8350 (t0) cc_final: 0.8093 (t0) REVERT: H 73 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8535 (mt-10) REVERT: I 90 ASP cc_start: 0.7362 (t0) cc_final: 0.7066 (t0) REVERT: I 126 ASN cc_start: 0.4593 (p0) cc_final: 0.4222 (p0) REVERT: I 127 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6497 (t80) REVERT: J 31 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8602 (mp) REVERT: J 44 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8824 (mt) REVERT: J 73 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8524 (mt-10) REVERT: J 93 GLN cc_start: 0.5475 (tm130) cc_final: 0.4758 (tm-30) REVERT: J 127 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6248 (t80) REVERT: K 93 GLN cc_start: 0.4821 (tm130) cc_final: 0.4523 (tm-30) REVERT: K 127 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6419 (t80) REVERT: L 60 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: L 133 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: M 94 THR cc_start: 0.6647 (OUTLIER) cc_final: 0.6307 (m) REVERT: M 108 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8902 (mt) REVERT: N 26 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8732 (mm) REVERT: N 96 TYR cc_start: 0.7574 (t80) cc_final: 0.6735 (t80) REVERT: N 127 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6143 (t80) REVERT: O 61 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7983 (mm-30) REVERT: P 39 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8589 (mt) REVERT: P 107 LYS cc_start: 0.8813 (mptt) cc_final: 0.8516 (mttm) REVERT: P 127 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.5896 (t80) REVERT: R 28 MET cc_start: 0.9137 (mmp) cc_final: 0.8901 (mmt) REVERT: R 117 ASN cc_start: 0.8401 (t0) cc_final: 0.7959 (t0) REVERT: S 39 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8529 (mt) REVERT: S 133 GLU cc_start: 0.8339 (mp0) cc_final: 0.8023 (mp0) REVERT: T 42 PHE cc_start: 0.9094 (t80) cc_final: 0.8795 (t80) REVERT: T 89 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7279 (mp) REVERT: T 90 ASP cc_start: 0.6031 (t0) cc_final: 0.5739 (t0) outliers start: 96 outliers final: 69 residues processed: 563 average time/residue: 1.2105 time to fit residues: 773.6658 Evaluate side-chains 598 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 507 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 94 THR 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 106 LEU 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 90 ASP 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 50 VAL 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 90 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 133 GLU 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 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 106 LEU 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 45 ASP 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 I residue 154 VAL 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 60 MET 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 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 60 MET Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 133 GLU 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 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 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain P residue 39 ILE 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 103 THR Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain S residue 39 ILE 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 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR 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 239 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 126 ASN G 126 ASN H 93 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 HIS ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** 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 117 ASN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN O 55 GLN Q 119 ASN ** S 93 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.113081 restraints weight = 28709.127| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.32 r_work: 0.3138 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20960 Z= 0.248 Angle : 0.836 26.268 28580 Z= 0.384 Chirality : 0.053 0.197 3660 Planarity : 0.003 0.031 3760 Dihedral : 6.160 56.989 3044 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 4.96 % Allowed : 23.45 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2900 helix: 1.20 (0.20), residues: 540 sheet: 0.05 (0.18), residues: 960 loop : -2.80 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 82 PHE 0.009 0.002 PHE J 42 TYR 0.006 0.001 TYR D 96 ARG 0.003 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.06148 ( 860) hydrogen bonds : angle 4.81120 ( 2340) covalent geometry : bond 0.00614 (20960) covalent geometry : angle 0.83634 (28580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16741.83 seconds wall clock time: 288 minutes 10.90 seconds (17290.90 seconds total)