Starting phenix.real_space_refine on Tue Jun 17 23:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi2_40060/06_2025/8gi2_40060.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi2_40060/06_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_40060/06_2025/8gi2_40060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi2_40060/06_2025/8gi2_40060.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi2_40060/06_2025/8gi2_40060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi2_40060/06_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-5710/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: 5.53, per 1000 atoms: 0.27 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: 4.87 Conformation dependent library (CDL) restraints added in 2.7 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: 5.92 Time building geometry restraints manager: 5.80 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: 0.22 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 38.410 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.680 ------------------------------------------------------------------------------- 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 : 2.077 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: 0.9897 time to fit residues: 814.6193 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 : 2.167 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118630 restraints weight = 28048.746| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.32 r_work: 0.3317 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 2.868 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: 0.8893 (mt-10) cc_final: 0.8578 (mt-10) REVERT: A 143 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 61 GLU cc_start: 0.7568 (pp20) cc_final: 0.7330 (pp20) REVERT: C 90 ASP cc_start: 0.6814 (t0) cc_final: 0.6571 (t0) REVERT: C 127 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.6067 (t80) REVERT: C 133 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 31 ILE cc_start: 0.9065 (mt) cc_final: 0.8767 (mp) REVERT: D 143 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 162 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7686 (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: 0.8483 (mt-10) REVERT: G 90 ASP cc_start: 0.6862 (t0) cc_final: 0.6612 (t0) REVERT: H 63 ASP cc_start: 0.8456 (t0) cc_final: 0.8192 (t0) REVERT: H 73 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8663 (mt-10) REVERT: H 112 ASP cc_start: 0.8321 (m-30) cc_final: 0.7889 (m-30) REVERT: I 90 ASP cc_start: 0.7130 (t0) cc_final: 0.6791 (t0) REVERT: J 44 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8606 (mt) REVERT: J 73 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8578 (mt-10) REVERT: K 127 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6180 (t80) REVERT: L 133 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7813 (mp0) REVERT: M 73 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8770 (mt-10) REVERT: M 108 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8860 (mt) REVERT: N 81 ASP cc_start: 0.8720 (m-30) cc_final: 0.8322 (m-30) REVERT: N 127 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6087 (t80) REVERT: O 90 ASP cc_start: 0.6249 (t0) cc_final: 0.6030 (t0) REVERT: O 96 TYR cc_start: 0.7503 (t80) cc_final: 0.6990 (t80) REVERT: O 127 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6051 (t80) REVERT: R 63 ASP cc_start: 0.8637 (t0) cc_final: 0.8323 (t0) REVERT: R 127 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.5747 (t80) REVERT: S 94 THR cc_start: 0.6825 (t) cc_final: 0.6449 (m) REVERT: S 127 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.5919 (t80) REVERT: T 46 LEU cc_start: 0.8745 (tp) cc_final: 0.8531 (tt) REVERT: T 123 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7562 (t) REVERT: T 146 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8246 (mm-30) outliers start: 150 outliers final: 62 residues processed: 629 average time/residue: 1.3300 time to fit residues: 953.4201 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 : 2.107 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110389 restraints weight = 28264.261| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.27 r_work: 0.3199 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20960 Z= 0.225 Angle : 0.719 16.644 28580 Z= 0.358 Chirality : 0.051 0.174 3660 Planarity : 0.003 0.027 3760 Dihedral : 6.657 54.549 3060 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 8.45 % Allowed : 14.48 % Favored : 77.07 % 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: -2.04 (0.15), residues: 2900 helix: 0.61 (0.22), residues: 580 sheet: -0.16 (0.18), residues: 960 loop : -3.29 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 82 PHE 0.014 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 0.06168 ( 860) hydrogen bonds : angle 4.90453 ( 2340) covalent geometry : bond 0.00551 (20960) covalent geometry : angle 0.71920 (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 751 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 555 time to evaluate : 2.130 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: 0.8862 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 90 ASP cc_start: 0.6551 (t0) cc_final: 0.6302 (t0) REVERT: A 127 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 143 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8531 (mt-10) REVERT: A 144 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: B 103 THR cc_start: 0.6542 (OUTLIER) cc_final: 0.5940 (p) REVERT: B 144 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: C 26 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8821 (mm) REVERT: C 61 GLU cc_start: 0.7855 (pp20) cc_final: 0.7616 (pp20) REVERT: C 90 ASP cc_start: 0.7127 (t0) cc_final: 0.6612 (t0) REVERT: C 96 TYR cc_start: 0.7237 (t80) cc_final: 0.7011 (t80) REVERT: C 127 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6403 (t80) REVERT: C 133 GLU cc_start: 0.8202 (mt-10) cc_final: 0.8000 (mt-10) REVERT: D 31 ILE cc_start: 0.9094 (mt) cc_final: 0.8809 (mp) REVERT: D 90 ASP cc_start: 0.7075 (t0) cc_final: 0.6750 (t0) REVERT: D 127 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6372 (t80) REVERT: D 143 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8598 (mt-10) REVERT: E 26 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8944 (mm) REVERT: E 112 ASP cc_start: 0.8255 (m-30) cc_final: 0.7989 (m-30) REVERT: E 162 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7749 (mtpt) REVERT: F 90 ASP cc_start: 0.7366 (t0) cc_final: 0.7128 (t0) REVERT: F 133 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: G 90 ASP cc_start: 0.7114 (t0) cc_final: 0.6787 (t0) REVERT: H 73 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8596 (mt-10) REVERT: I 90 ASP cc_start: 0.7312 (t0) cc_final: 0.6822 (t0) REVERT: J 73 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8643 (mt-10) REVERT: J 133 GLU cc_start: 0.8717 (pt0) cc_final: 0.8456 (pt0) REVERT: K 96 TYR cc_start: 0.7442 (t80) cc_final: 0.6940 (t80) REVERT: K 127 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6321 (t80) REVERT: L 144 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: M 108 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8933 (mt) REVERT: N 81 ASP cc_start: 0.8662 (m-30) cc_final: 0.8314 (m-30) REVERT: N 96 TYR cc_start: 0.7898 (t80) cc_final: 0.7525 (t80) REVERT: N 127 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6400 (t80) REVERT: N 143 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8639 (mt-10) REVERT: O 90 ASP cc_start: 0.6597 (t0) cc_final: 0.6193 (t0) REVERT: O 108 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (mp) REVERT: O 127 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6371 (t80) REVERT: Q 46 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8641 (tt) REVERT: R 127 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.6076 (t80) REVERT: S 46 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8688 (tp) REVERT: S 90 ASP cc_start: 0.5764 (t0) cc_final: 0.5364 (t0) REVERT: S 133 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8259 (mp0) REVERT: T 90 ASP cc_start: 0.6093 (t0) cc_final: 0.5866 (t0) REVERT: T 101 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7595 (mmtm) outliers start: 196 outliers final: 88 residues processed: 632 average time/residue: 1.2523 time to fit residues: 899.3069 Evaluate side-chains 641 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 534 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 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 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 103 THR 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 F residue 133 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 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 119 ASN 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 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 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: 10.0000 chunk 149 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN F 52 ASN G 52 ASN K 119 ASN L 55 GLN N 119 ASN Q 93 GLN Q 126 ASN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN S 126 ASN ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114806 restraints weight = 28473.015| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.27 r_work: 0.3247 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20960 Z= 0.154 Angle : 0.674 17.484 28580 Z= 0.330 Chirality : 0.049 0.159 3660 Planarity : 0.002 0.026 3760 Dihedral : 6.366 55.009 3056 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 7.93 % Allowed : 17.24 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2900 helix: 0.90 (0.22), residues: 580 sheet: -0.03 (0.18), residues: 960 loop : -2.98 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS Q 82 PHE 0.009 0.001 PHE P 42 TYR 0.007 0.001 TYR F 127 ARG 0.001 0.000 ARG I 148 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 860) hydrogen bonds : angle 4.72685 ( 2340) covalent geometry : bond 0.00363 (20960) covalent geometry : angle 0.67351 (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 725 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 541 time to evaluate : 2.365 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: 0.8850 (mt-10) cc_final: 0.8593 (mt-10) REVERT: A 90 ASP cc_start: 0.6999 (t0) cc_final: 0.6727 (t0) REVERT: A 127 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.6288 (t80) REVERT: A 143 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 103 THR cc_start: 0.6378 (OUTLIER) cc_final: 0.5788 (p) REVERT: C 26 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8776 (mm) REVERT: C 61 GLU cc_start: 0.7762 (pp20) cc_final: 0.7534 (pp20) REVERT: C 90 ASP cc_start: 0.7151 (t0) cc_final: 0.6733 (t0) REVERT: C 127 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6170 (t80) REVERT: D 31 ILE cc_start: 0.9085 (mt) cc_final: 0.8814 (mp) REVERT: D 143 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 162 LYS cc_start: 0.8265 (mtmt) cc_final: 0.7773 (mttt) REVERT: E 26 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8915 (mm) REVERT: E 112 ASP cc_start: 0.8151 (m-30) cc_final: 0.7873 (m-30) REVERT: E 162 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7621 (mtpt) REVERT: F 90 ASP cc_start: 0.7570 (t0) cc_final: 0.7171 (t0) REVERT: F 133 GLU cc_start: 0.8711 (pm20) cc_final: 0.8206 (pt0) REVERT: G 90 ASP cc_start: 0.7212 (t0) cc_final: 0.6878 (t0) REVERT: G 144 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: H 73 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8591 (mt-10) REVERT: I 90 ASP cc_start: 0.7358 (t0) cc_final: 0.6827 (t0) REVERT: J 73 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8672 (mt-10) REVERT: J 127 TYR cc_start: 0.7589 (OUTLIER) cc_final: 0.6288 (t80) REVERT: J 133 GLU cc_start: 0.8686 (pt0) cc_final: 0.8443 (pt0) REVERT: K 127 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6230 (t80) REVERT: L 61 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: L 90 ASP cc_start: 0.6769 (t0) cc_final: 0.6334 (t0) REVERT: L 133 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: M 108 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8949 (mt) REVERT: N 96 TYR cc_start: 0.7598 (t80) cc_final: 0.6990 (t80) REVERT: N 127 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6292 (t80) REVERT: N 143 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8671 (mt-10) REVERT: O 108 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8941 (mp) REVERT: O 127 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6255 (t80) REVERT: Q 46 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (tt) REVERT: T 90 ASP cc_start: 0.6037 (t0) cc_final: 0.5790 (t0) outliers start: 184 outliers final: 85 residues processed: 617 average time/residue: 1.2973 time to fit residues: 904.6915 Evaluate side-chains 630 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 530 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 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 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 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 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 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 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 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 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 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 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 212 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN T 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114518 restraints weight = 28363.131| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.27 r_work: 0.3259 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20960 Z= 0.160 Angle : 0.680 20.652 28580 Z= 0.330 Chirality : 0.049 0.161 3660 Planarity : 0.002 0.026 3760 Dihedral : 6.300 55.127 3056 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 8.06 % Allowed : 18.15 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2900 helix: 1.02 (0.21), residues: 580 sheet: -0.00 (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 O 82 PHE 0.007 0.001 PHE P 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 0.05162 ( 860) hydrogen bonds : angle 4.70434 ( 2340) covalent geometry : bond 0.00382 (20960) covalent geometry : angle 0.67984 (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 725 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 538 time to evaluate : 2.386 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: 0.9257 (mp) cc_final: 0.9052 (mp) REVERT: A 73 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8593 (mt-10) REVERT: A 90 ASP cc_start: 0.6996 (t0) cc_final: 0.6684 (t0) REVERT: A 127 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6393 (t80) REVERT: A 143 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8625 (mt-10) REVERT: B 103 THR cc_start: 0.6285 (OUTLIER) cc_final: 0.5660 (p) REVERT: C 26 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8791 (mm) REVERT: C 61 GLU cc_start: 0.7812 (pp20) cc_final: 0.7559 (pp20) REVERT: C 90 ASP cc_start: 0.7162 (t0) cc_final: 0.6777 (t0) REVERT: C 127 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6312 (t80) REVERT: D 31 ILE cc_start: 0.9102 (mt) cc_final: 0.8843 (mp) REVERT: D 143 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8571 (mt-10) REVERT: D 145 ASP cc_start: 0.8219 (m-30) cc_final: 0.7984 (m-30) REVERT: D 162 LYS cc_start: 0.8313 (mtmt) cc_final: 0.7802 (mttt) REVERT: E 26 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8944 (mm) REVERT: E 90 ASP cc_start: 0.6507 (t0) cc_final: 0.6041 (p0) REVERT: E 93 GLN cc_start: 0.6071 (tm130) cc_final: 0.5776 (tm-30) REVERT: E 112 ASP cc_start: 0.8200 (m-30) cc_final: 0.7912 (m-30) REVERT: E 162 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7760 (mtpt) REVERT: F 90 ASP cc_start: 0.7613 (t0) cc_final: 0.7136 (t0) REVERT: F 133 GLU cc_start: 0.8735 (pm20) cc_final: 0.8234 (pt0) REVERT: F 144 GLU cc_start: 0.8826 (pt0) cc_final: 0.8607 (pt0) REVERT: G 90 ASP cc_start: 0.7241 (t0) cc_final: 0.6869 (t0) REVERT: G 103 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6622 (m) REVERT: G 144 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: H 63 ASP cc_start: 0.8568 (t0) cc_final: 0.8321 (t0) REVERT: H 73 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8598 (mt-10) REVERT: I 90 ASP cc_start: 0.7275 (t0) cc_final: 0.6681 (t0) REVERT: J 73 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8717 (mt-10) REVERT: J 133 GLU cc_start: 0.8675 (pt0) cc_final: 0.8475 (pt0) REVERT: K 64 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: K 96 TYR cc_start: 0.7308 (t80) cc_final: 0.6768 (t80) REVERT: K 127 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.6227 (t80) REVERT: L 61 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7357 (pp20) REVERT: L 133 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: L 144 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: M 108 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8910 (mt) REVERT: N 96 TYR cc_start: 0.7531 (t80) cc_final: 0.6969 (t80) REVERT: N 127 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6365 (t80) REVERT: N 143 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8766 (mt-10) REVERT: O 61 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8189 (mm-30) REVERT: O 64 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: O 127 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6237 (t80) REVERT: P 127 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.5978 (t80) REVERT: Q 89 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (mp) REVERT: T 90 ASP cc_start: 0.6194 (t0) cc_final: 0.5883 (t0) outliers start: 187 outliers final: 99 residues processed: 615 average time/residue: 1.4507 time to fit residues: 1011.5483 Evaluate side-chains 644 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 527 time to evaluate : 2.717 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 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 50 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 50 VAL 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 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 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 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 59 ASN Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 23 ILE 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 106 LEU 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 50 VAL Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 56 optimal weight: 0.6980 chunk 259 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 164 optimal weight: 0.0020 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 55 GLN L 93 GLN ** R 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.125453 restraints weight = 27846.155| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.41 r_work: 0.3306 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20960 Z= 0.116 Angle : 0.651 19.743 28580 Z= 0.313 Chirality : 0.047 0.147 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.872 55.849 3054 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 6.72 % Allowed : 20.00 % Favored : 73.28 % 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: -1.40 (0.15), residues: 2900 helix: 1.38 (0.21), residues: 560 sheet: 0.10 (0.18), residues: 960 loop : -2.83 (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 0.000 0.000 ARG G 148 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 860) hydrogen bonds : angle 4.53473 ( 2340) covalent geometry : bond 0.00253 (20960) covalent geometry : angle 0.65086 (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 693 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 537 time to evaluate : 2.457 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: 0.9272 (OUTLIER) cc_final: 0.9064 (mp) REVERT: A 73 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 96 TYR cc_start: 0.7217 (t80) cc_final: 0.6770 (t80) REVERT: A 127 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6379 (t80) REVERT: A 143 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8518 (mt-10) REVERT: B 103 THR cc_start: 0.6116 (OUTLIER) cc_final: 0.5507 (p) REVERT: C 26 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8821 (mm) REVERT: C 61 GLU cc_start: 0.7695 (pp20) cc_final: 0.7463 (pp20) REVERT: C 90 ASP cc_start: 0.7025 (t0) cc_final: 0.6708 (t0) REVERT: C 93 GLN cc_start: 0.5840 (tm130) cc_final: 0.5562 (tm-30) REVERT: C 127 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6496 (t80) REVERT: D 31 ILE cc_start: 0.9079 (mt) cc_final: 0.8842 (mp) REVERT: D 143 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8545 (mt-10) REVERT: D 145 ASP cc_start: 0.8099 (m-30) cc_final: 0.7888 (m-30) REVERT: D 162 LYS cc_start: 0.8275 (mtmt) cc_final: 0.7760 (mttt) REVERT: E 26 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8893 (mm) REVERT: E 90 ASP cc_start: 0.6451 (t0) cc_final: 0.6044 (p0) REVERT: E 93 GLN cc_start: 0.5797 (tm130) cc_final: 0.5540 (tm-30) REVERT: E 112 ASP cc_start: 0.8169 (m-30) cc_final: 0.7907 (m-30) REVERT: E 162 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7733 (mtpt) REVERT: F 90 ASP cc_start: 0.7627 (t0) cc_final: 0.7207 (t0) REVERT: F 133 GLU cc_start: 0.8703 (pm20) cc_final: 0.8183 (pt0) REVERT: F 144 GLU cc_start: 0.8776 (pt0) cc_final: 0.8548 (pt0) REVERT: G 90 ASP cc_start: 0.7248 (t0) cc_final: 0.6922 (t0) REVERT: H 63 ASP cc_start: 0.8365 (t0) cc_final: 0.8142 (t0) REVERT: H 73 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8599 (mt-10) REVERT: I 59 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7917 (p0) REVERT: I 61 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7850 (mp0) REVERT: I 90 ASP cc_start: 0.7252 (t0) cc_final: 0.6641 (t0) REVERT: J 31 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8623 (mp) REVERT: J 44 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8787 (mt) REVERT: J 73 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8661 (mt-10) REVERT: J 133 GLU cc_start: 0.8671 (pt0) cc_final: 0.8462 (pt0) REVERT: K 127 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6355 (t80) REVERT: L 133 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: M 108 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8889 (mt) REVERT: N 96 TYR cc_start: 0.7527 (t80) cc_final: 0.6832 (t80) REVERT: N 127 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6305 (t80) REVERT: N 143 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8733 (mt-10) REVERT: O 61 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8006 (mm-30) REVERT: O 64 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: O 127 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.5953 (t80) REVERT: P 96 TYR cc_start: 0.7235 (t80) cc_final: 0.6444 (t80) REVERT: P 107 LYS cc_start: 0.8913 (mptt) cc_final: 0.8596 (mttm) REVERT: P 127 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5952 (t80) REVERT: S 133 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: T 90 ASP cc_start: 0.6089 (t0) cc_final: 0.5795 (t0) outliers start: 156 outliers final: 68 residues processed: 606 average time/residue: 1.7127 time to fit residues: 1189.6669 Evaluate side-chains 601 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 516 time to evaluate : 2.713 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 26 ILE 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 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 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 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 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 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain O residue 133 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 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 T residue 50 VAL 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: 7.9990 chunk 86 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN O 55 GLN R 119 ASN ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN T 119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120869 restraints weight = 28408.059| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.37 r_work: 0.3218 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20960 Z= 0.124 Angle : 0.661 19.000 28580 Z= 0.315 Chirality : 0.048 0.165 3660 Planarity : 0.002 0.025 3760 Dihedral : 5.666 55.823 3050 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 6.42 % Allowed : 20.91 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.15), residues: 2900 helix: 1.54 (0.21), residues: 520 sheet: 0.18 (0.18), residues: 960 loop : -2.79 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.006 0.001 PHE P 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 0.04392 ( 860) hydrogen bonds : angle 4.53650 ( 2340) covalent geometry : bond 0.00283 (20960) covalent geometry : angle 0.66139 (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 674 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 525 time to evaluate : 2.563 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: A 31 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8980 (mp) REVERT: A 73 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8558 (mt-10) REVERT: A 90 ASP cc_start: 0.6864 (t0) cc_final: 0.6642 (OUTLIER) REVERT: A 126 ASN cc_start: 0.6181 (p0) cc_final: 0.5960 (p0) REVERT: A 127 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6174 (t80) REVERT: A 143 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8563 (mt-10) REVERT: B 103 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5460 (p) REVERT: C 26 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 61 GLU cc_start: 0.7654 (pp20) cc_final: 0.7366 (pp20) REVERT: C 90 ASP cc_start: 0.6896 (t0) cc_final: 0.6615 (t0) REVERT: C 93 GLN cc_start: 0.6065 (tm130) cc_final: 0.5719 (tm-30) REVERT: C 106 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6155 (mm) REVERT: C 127 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6428 (t80) REVERT: D 31 ILE cc_start: 0.9089 (mt) cc_final: 0.8872 (mp) REVERT: D 143 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8559 (mt-10) REVERT: D 145 ASP cc_start: 0.8174 (m-30) cc_final: 0.7908 (m-30) REVERT: D 162 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7755 (mttt) REVERT: E 26 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8872 (mm) REVERT: E 93 GLN cc_start: 0.5814 (tm130) cc_final: 0.5498 (tm-30) REVERT: E 112 ASP cc_start: 0.8227 (m-30) cc_final: 0.7956 (m-30) REVERT: E 162 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7697 (mtpt) REVERT: F 59 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8288 (p0) REVERT: F 127 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: F 133 GLU cc_start: 0.8669 (pm20) cc_final: 0.8102 (pt0) REVERT: F 144 GLU cc_start: 0.8835 (pt0) cc_final: 0.8593 (pt0) REVERT: G 90 ASP cc_start: 0.7309 (t0) cc_final: 0.6940 (t0) REVERT: G 103 THR cc_start: 0.6684 (OUTLIER) cc_final: 0.6315 (m) REVERT: H 63 ASP cc_start: 0.8335 (t0) cc_final: 0.8109 (t0) REVERT: H 73 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8515 (mt-10) REVERT: I 59 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7959 (p0) REVERT: I 61 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7799 (mp0) REVERT: I 90 ASP cc_start: 0.7385 (t0) cc_final: 0.6919 (t0) REVERT: J 31 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8623 (mp) REVERT: J 44 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (mt) REVERT: J 73 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8648 (mt-10) REVERT: J 96 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6506 (t80) REVERT: J 133 GLU cc_start: 0.8687 (pt0) cc_final: 0.8467 (pt0) REVERT: K 64 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: K 96 TYR cc_start: 0.7271 (t80) cc_final: 0.6733 (t80) REVERT: K 127 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6350 (t80) REVERT: L 133 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (mp0) REVERT: M 61 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: M 94 THR cc_start: 0.6612 (OUTLIER) cc_final: 0.6302 (m) REVERT: M 108 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8935 (mt) REVERT: N 64 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7840 (mt-10) REVERT: N 96 TYR cc_start: 0.7568 (t80) cc_final: 0.6814 (t80) REVERT: N 127 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6253 (t80) REVERT: N 143 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8712 (mt-10) REVERT: O 61 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8034 (mm-30) REVERT: O 64 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: O 127 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6091 (t80) REVERT: P 61 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: P 96 TYR cc_start: 0.7238 (t80) cc_final: 0.6412 (t80) REVERT: P 127 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.5912 (t80) REVERT: S 133 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: T 90 ASP cc_start: 0.6171 (t0) cc_final: 0.5903 (t0) outliers start: 149 outliers final: 79 residues processed: 590 average time/residue: 1.9046 time to fit residues: 1278.1224 Evaluate side-chains 613 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 509 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 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU 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 26 ILE Chi-restraints excluded: chain C residue 106 LEU 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 D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 59 ASN 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 60 MET 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 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 I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 96 TYR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 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 26 ILE Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 145 ASP Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU 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 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 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 T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN 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: 9.9990 chunk 181 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 221 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN I 82 HIS ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN O 82 HIS ** O 93 GLN ** 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 ** T 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111130 restraints weight = 28663.111| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.24 r_work: 0.3210 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20960 Z= 0.277 Angle : 0.809 20.339 28580 Z= 0.387 Chirality : 0.054 0.176 3660 Planarity : 0.003 0.032 3760 Dihedral : 6.583 55.383 3050 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.11 % Allowed : 20.47 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.56 (0.15), residues: 2900 helix: 0.99 (0.20), residues: 580 sheet: -0.04 (0.18), residues: 960 loop : -2.82 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS M 82 PHE 0.008 0.002 PHE J 159 TYR 0.010 0.001 TYR F 96 ARG 0.003 0.001 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.06478 ( 860) hydrogen bonds : angle 4.87655 ( 2340) covalent geometry : bond 0.00689 (20960) covalent geometry : angle 0.80870 (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 694 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 529 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8598 (mt-10) REVERT: A 90 ASP cc_start: 0.6778 (t0) cc_final: 0.6570 (t0) REVERT: A 126 ASN cc_start: 0.6513 (p0) cc_final: 0.6272 (p0) REVERT: A 127 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 90 ASP cc_start: 0.7018 (t0) cc_final: 0.6739 (t0) REVERT: B 103 THR cc_start: 0.6498 (OUTLIER) cc_final: 0.5910 (p) REVERT: C 26 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 61 GLU cc_start: 0.8060 (pp20) cc_final: 0.7740 (pp20) REVERT: C 90 ASP cc_start: 0.6930 (t0) cc_final: 0.6525 (t0) REVERT: C 93 GLN cc_start: 0.6589 (tm130) cc_final: 0.6327 (tm-30) REVERT: C 106 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5578 (mm) REVERT: C 127 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6597 (t80) REVERT: D 31 ILE cc_start: 0.9193 (mt) cc_final: 0.8916 (mp) REVERT: D 145 ASP cc_start: 0.8234 (m-30) cc_final: 0.7976 (m-30) REVERT: D 162 LYS cc_start: 0.8307 (mtmt) cc_final: 0.8056 (mmmt) REVERT: E 26 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8962 (mm) REVERT: E 112 ASP cc_start: 0.8175 (m-30) cc_final: 0.7906 (m-30) REVERT: E 162 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7818 (mtpt) REVERT: F 90 ASP cc_start: 0.7407 (t0) cc_final: 0.6928 (t0) REVERT: F 133 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: F 144 GLU cc_start: 0.8853 (pt0) cc_final: 0.8577 (pt0) REVERT: G 90 ASP cc_start: 0.7258 (t0) cc_final: 0.6970 (t0) REVERT: G 93 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6516 (tm130) REVERT: I 90 ASP cc_start: 0.7204 (t0) cc_final: 0.6629 (t0) REVERT: J 28 MET cc_start: 0.9439 (mmp) cc_final: 0.9224 (mmm) REVERT: J 73 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8617 (mt-10) REVERT: K 64 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: K 127 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6334 (t80) REVERT: L 144 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: M 108 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8897 (mt) REVERT: N 127 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.6246 (t80) REVERT: O 64 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: O 90 ASP cc_start: 0.6607 (t0) cc_final: 0.6166 (t0) REVERT: P 127 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.5954 (t80) REVERT: T 89 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7314 (mp) outliers start: 165 outliers final: 91 residues processed: 602 average time/residue: 1.3972 time to fit residues: 953.2751 Evaluate side-chains 617 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 510 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER 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 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 C residue 26 ILE 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 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 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 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 94 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 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 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 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 94 THR Chi-restraints excluded: chain L residue 106 LEU 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 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 155 ASP Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 106 LEU 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 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 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 chunk 269 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN E 126 ASN G 59 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN O 126 ASN P 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121423 restraints weight = 28066.006| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.35 r_work: 0.3234 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20960 Z= 0.165 Angle : 0.748 23.087 28580 Z= 0.350 Chirality : 0.050 0.160 3660 Planarity : 0.003 0.029 3760 Dihedral : 6.136 56.522 3048 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 5.47 % Allowed : 22.41 % Favored : 72.11 % 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: 1.25 (0.20), residues: 540 sheet: -0.01 (0.18), residues: 960 loop : -2.83 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 82 PHE 0.019 0.001 PHE R 42 TYR 0.007 0.001 TYR N 96 ARG 0.001 0.000 ARG B 148 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 860) hydrogen bonds : angle 4.73849 ( 2340) covalent geometry : bond 0.00396 (20960) covalent geometry : angle 0.74831 (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 649 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 522 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 90 ASP cc_start: 0.6919 (t0) cc_final: 0.6599 (t0) REVERT: A 126 ASN cc_start: 0.6607 (p0) cc_final: 0.6368 (p0) REVERT: A 127 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6183 (t80) REVERT: B 90 ASP cc_start: 0.6785 (t0) cc_final: 0.6570 (t0) REVERT: B 103 THR cc_start: 0.6238 (OUTLIER) cc_final: 0.5622 (p) REVERT: C 26 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (mm) REVERT: C 61 GLU cc_start: 0.7913 (pp20) cc_final: 0.7567 (pp20) REVERT: C 90 ASP cc_start: 0.7054 (t0) cc_final: 0.6669 (t0) REVERT: C 93 GLN cc_start: 0.6446 (tm130) cc_final: 0.6176 (tm-30) REVERT: C 105 LYS cc_start: 0.5433 (pmtt) cc_final: 0.5222 (pmtt) REVERT: C 106 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5824 (mm) REVERT: C 127 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6749 (t80) REVERT: D 31 ILE cc_start: 0.9139 (mt) cc_final: 0.8867 (mp) REVERT: D 145 ASP cc_start: 0.8162 (m-30) cc_final: 0.7880 (m-30) REVERT: D 162 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7995 (mmmt) REVERT: E 26 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8930 (mm) REVERT: E 112 ASP cc_start: 0.8199 (m-30) cc_final: 0.7903 (m-30) REVERT: E 162 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7786 (mtpt) REVERT: F 133 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: F 144 GLU cc_start: 0.8865 (pt0) cc_final: 0.8575 (pt0) REVERT: G 90 ASP cc_start: 0.7258 (t0) cc_final: 0.6957 (t0) REVERT: G 103 THR cc_start: 0.6905 (OUTLIER) cc_final: 0.6573 (m) REVERT: H 73 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8624 (mt-10) REVERT: I 90 ASP cc_start: 0.7300 (t0) cc_final: 0.6678 (t0) REVERT: I 127 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6476 (t80) REVERT: I 133 GLU cc_start: 0.8453 (pt0) cc_final: 0.8121 (pt0) REVERT: J 31 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8642 (mp) REVERT: J 73 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8611 (mt-10) REVERT: K 64 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: K 127 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.6266 (t80) REVERT: L 60 MET cc_start: 0.9016 (mtm) cc_final: 0.8563 (mtm) REVERT: L 61 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: L 144 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: M 61 GLU cc_start: 0.7647 (mp0) cc_final: 0.7399 (mp0) REVERT: M 108 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8887 (mt) REVERT: N 144 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: O 55 GLN cc_start: 0.8775 (mt0) cc_final: 0.8506 (mt0) REVERT: O 61 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: O 64 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: P 96 TYR cc_start: 0.7370 (t80) cc_final: 0.6590 (t80) REVERT: P 107 LYS cc_start: 0.8887 (mptt) cc_final: 0.8553 (mttm) REVERT: P 127 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.5981 (t80) REVERT: S 89 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7585 (pp) REVERT: S 90 ASP cc_start: 0.6498 (t0) cc_final: 0.6215 (t0) REVERT: T 90 ASP cc_start: 0.5783 (t0) cc_final: 0.5425 (t0) outliers start: 127 outliers final: 76 residues processed: 577 average time/residue: 1.4124 time to fit residues: 925.0307 Evaluate side-chains 606 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 510 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER 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 127 TYR 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 26 ILE 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 103 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 94 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 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 90 ASP 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 45 ASP 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 144 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain 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 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 S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain S residue 147 THR Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL 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: 3.9990 chunk 248 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3632 r_free = 0.3632 target = 0.144707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118191 restraints weight = 28508.989| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.36 r_work: 0.3186 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20960 Z= 0.145 Angle : 0.735 23.072 28580 Z= 0.342 Chirality : 0.049 0.172 3660 Planarity : 0.002 0.028 3760 Dihedral : 5.847 57.192 3044 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 4.70 % Allowed : 23.45 % Favored : 71.85 % 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: -1.41 (0.15), residues: 2900 helix: 1.25 (0.20), residues: 580 sheet: 0.07 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 82 PHE 0.005 0.001 PHE J 42 TYR 0.006 0.001 TYR N 127 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 860) hydrogen bonds : angle 4.68981 ( 2340) covalent geometry : bond 0.00345 (20960) covalent geometry : angle 0.73550 (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 629 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 520 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8505 (mt-10) REVERT: A 90 ASP cc_start: 0.6854 (t0) cc_final: 0.6489 (t0) REVERT: B 90 ASP cc_start: 0.6734 (t0) cc_final: 0.6417 (t0) REVERT: B 103 THR cc_start: 0.6156 (OUTLIER) cc_final: 0.5544 (p) REVERT: C 26 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 61 GLU cc_start: 0.7839 (pp20) cc_final: 0.7514 (pp20) REVERT: C 90 ASP cc_start: 0.7019 (t0) cc_final: 0.6603 (t0) REVERT: C 93 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.6036 (tm-30) REVERT: C 106 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5777 (mm) REVERT: C 127 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6687 (t80) REVERT: D 31 ILE cc_start: 0.9096 (mt) cc_final: 0.8866 (mp) REVERT: D 145 ASP cc_start: 0.8192 (m-30) cc_final: 0.7890 (m-30) REVERT: D 162 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8026 (mmmt) REVERT: E 26 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8897 (mm) REVERT: E 112 ASP cc_start: 0.8216 (m-30) cc_final: 0.7901 (m-30) REVERT: E 162 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7799 (mtpt) REVERT: F 90 ASP cc_start: 0.7316 (t0) cc_final: 0.6906 (t0) REVERT: F 133 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: F 144 GLU cc_start: 0.8892 (pt0) cc_final: 0.8617 (pt0) REVERT: G 90 ASP cc_start: 0.7410 (t0) cc_final: 0.7179 (t0) REVERT: G 103 THR cc_start: 0.6682 (OUTLIER) cc_final: 0.6379 (m) REVERT: H 73 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8583 (mt-10) REVERT: I 59 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7901 (p0) REVERT: I 61 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7939 (mp0) REVERT: I 90 ASP cc_start: 0.7311 (t0) cc_final: 0.6646 (t0) REVERT: I 127 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6540 (t80) REVERT: I 133 GLU cc_start: 0.8440 (pt0) cc_final: 0.8094 (pt0) REVERT: J 31 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8601 (mp) REVERT: J 73 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8548 (mt-10) REVERT: K 64 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: K 96 TYR cc_start: 0.7337 (t80) cc_final: 0.6781 (t80) REVERT: K 127 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.6401 (t80) REVERT: L 60 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8313 (mtm) REVERT: L 61 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: M 61 GLU cc_start: 0.7724 (mp0) cc_final: 0.7414 (mp0) REVERT: M 94 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6329 (m) REVERT: M 108 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8848 (mt) REVERT: N 93 GLN cc_start: 0.7158 (mt0) cc_final: 0.6789 (pt0) REVERT: N 144 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: O 55 GLN cc_start: 0.8761 (mt0) cc_final: 0.8471 (mt0) REVERT: O 61 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: O 64 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: P 107 LYS cc_start: 0.8838 (mptt) cc_final: 0.8533 (mttm) REVERT: P 127 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.5941 (t80) REVERT: S 89 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7496 (pp) outliers start: 109 outliers final: 73 residues processed: 562 average time/residue: 1.3114 time to fit residues: 832.8493 Evaluate side-chains 608 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 513 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER 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 127 TYR 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 26 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 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 94 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 133 GLU 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 106 LEU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP 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 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 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 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 61 GLU Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE 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 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 147 THR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 94 THR Chi-restraints excluded: chain T residue 50 VAL 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: 0.8980 chunk 264 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118707 restraints weight = 28772.380| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.37 r_work: 0.3193 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20960 Z= 0.143 Angle : 0.733 23.489 28580 Z= 0.341 Chirality : 0.049 0.166 3660 Planarity : 0.002 0.026 3760 Dihedral : 5.750 57.630 3044 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.83 % Allowed : 23.28 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.20), residues: 580 sheet: 0.12 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 82 PHE 0.021 0.001 PHE R 42 TYR 0.005 0.001 TYR J 156 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.04809 ( 860) hydrogen bonds : angle 4.65562 ( 2340) covalent geometry : bond 0.00339 (20960) covalent geometry : angle 0.73286 (28580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19435.83 seconds wall clock time: 345 minutes 10.25 seconds (20710.25 seconds total)