Starting phenix.real_space_refine on Sat Aug 23 09:18:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofh_20046/08_2025/6ofh_20046.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.023 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: 3 Type Number sf(0) Gaussians C 7353 2.51 5 N 1919 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11628 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Restraints were copied for chains: U, V, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 0.94, per 1000 atoms: 0.08 Number of scatterers: 11628 At special positions: 0 Unit cell: (93.94, 92.232, 153.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2356 8.00 N 1919 7.00 C 7353 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: 0.89 Conformation dependent library (CDL) restraints added in 383.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2888 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 88.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE U 16 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP U 17 " --> pdb=" O SER U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 36 " --> pdb=" O ASP U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 56 " --> pdb=" O SER U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN U 77 " --> pdb=" O ALA U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE V 16 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP V 17 " --> pdb=" O SER V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR V 28 " --> pdb=" O GLN V 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU V 56 " --> pdb=" O SER V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN V 77 " --> pdb=" O ALA V 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 56 " --> pdb=" O SER E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN E 77 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN G 77 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 4.574A pdb=" N GLN H 77 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 56 " --> pdb=" O SER I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN I 77 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA J 46 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 56 " --> pdb=" O SER J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 56 " --> pdb=" O SER K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA L 46 " --> pdb=" O ALA L 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU L 56 " --> pdb=" O SER L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN L 77 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU M 56 " --> pdb=" O SER M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN M 77 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA N 46 " --> pdb=" O ALA N 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN N 77 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 56 " --> pdb=" O SER O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN O 77 " --> pdb=" O ALA O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.742A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU Q 56 " --> pdb=" O SER Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN Q 77 " --> pdb=" O ALA Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 73 removed outlier: 3.681A pdb=" N ALA R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 56 " --> pdb=" O SER R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN R 77 " --> pdb=" O ALA R 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 36 removed outlier: 3.750A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA S 36 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU S 56 " --> pdb=" O SER S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 4.576A pdb=" N GLN S 77 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 20 removed outlier: 3.743A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.751A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA T 36 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 73 removed outlier: 3.682A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU T 56 " --> pdb=" O SER T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 removed outlier: 4.575A pdb=" N GLN T 77 " --> pdb=" O ALA T 74 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2565 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: 1.81 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2071 1.29 - 1.35: 1767 1.35 - 1.41: 1130 1.41 - 1.48: 1777 1.48 - 1.54: 5092 Bond restraints: 11837 Sorted by residual: bond pdb=" CB GLU M 53 " pdb=" CG GLU M 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB GLU R 53 " pdb=" CG GLU R 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 bond pdb=" CB GLU J 53 " pdb=" CG GLU J 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 11832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15378 1.64 - 3.28: 690 3.28 - 4.92: 25 4.92 - 6.56: 0 6.56 - 8.21: 19 Bond angle restraints: 16112 Sorted by residual: angle pdb=" CA LEU N 56 " pdb=" CB LEU N 56 " pdb=" CG LEU N 56 " ideal model delta sigma weight residual 116.30 108.09 8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU L 56 " pdb=" CB LEU L 56 " pdb=" CG LEU L 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" CA LEU K 56 " pdb=" CB LEU K 56 " pdb=" CG LEU K 56 " ideal model delta sigma weight residual 116.30 108.10 8.20 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA PRO H 38 " pdb=" C PRO H 38 " pdb=" O PRO H 38 " ideal model delta sigma weight residual 121.38 119.58 1.80 7.70e-01 1.69e+00 5.47e+00 angle pdb=" CA LEU J 56 " pdb=" CB LEU J 56 " pdb=" CG LEU J 56 " ideal model delta sigma weight residual 116.30 108.12 8.18 3.50e+00 8.16e-02 5.47e+00 ... (remaining 16107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.17: 5624 6.17 - 12.34: 1119 12.34 - 18.51: 324 18.51 - 24.68: 77 24.68 - 30.85: 38 Dihedral angle restraints: 7182 sinusoidal: 2755 harmonic: 4427 Sorted by residual: dihedral pdb=" CA ASP D 70 " pdb=" C ASP D 70 " pdb=" N ILE D 71 " pdb=" CA ILE D 71 " ideal model delta harmonic sigma weight residual 180.00 164.46 15.54 0 5.00e+00 4.00e-02 9.66e+00 dihedral pdb=" CA ASP Q 70 " pdb=" C ASP Q 70 " pdb=" N ILE Q 71 " pdb=" CA ILE Q 71 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.65e+00 dihedral pdb=" CA ASP S 70 " pdb=" C ASP S 70 " pdb=" N ILE S 71 " pdb=" CA ILE S 71 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.64e+00 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 423 0.020 - 0.041: 702 0.041 - 0.061: 378 0.061 - 0.082: 212 0.082 - 0.102: 128 Chirality restraints: 1843 Sorted by residual: chirality pdb=" CA SER N 39 " pdb=" N SER N 39 " pdb=" C SER N 39 " pdb=" CB SER N 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA SER U 39 " pdb=" N SER U 39 " pdb=" C SER U 39 " pdb=" CB SER U 39 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.60e-01 chirality pdb=" CA PRO U 38 " pdb=" N PRO U 38 " pdb=" C PRO U 38 " pdb=" CB PRO U 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 1840 not shown) Planarity restraints: 2109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 76 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE P 76 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE P 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN P 77 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 76 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE R 76 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE R 76 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN R 77 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 76 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE O 76 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE O 76 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN O 77 " 0.009 2.00e-02 2.50e+03 ... (remaining 2106 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 106 2.66 - 3.22: 11323 3.22 - 3.78: 17158 3.78 - 4.34: 24963 4.34 - 4.90: 40716 Nonbonded interactions: 94266 Sorted by model distance: nonbonded pdb=" OD1 ASP D 10 " pdb=" OG SER H 49 " model vdw 2.097 3.040 nonbonded pdb=" NZ LYS G 66 " pdb=" OD2 ASP G 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS F 66 " pdb=" OD2 ASP F 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS P 66 " pdb=" OD2 ASP P 70 " model vdw 2.098 3.120 nonbonded pdb=" NZ LYS L 66 " pdb=" OD2 ASP L 70 " model vdw 2.098 3.120 ... (remaining 94261 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: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'U' selection = chain 'V' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.040 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.035 11837 Z= 0.339 Angle : 0.752 8.205 16112 Z= 0.416 Chirality : 0.045 0.102 1843 Planarity : 0.005 0.028 2109 Dihedral : 7.705 30.854 4294 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.76 (0.10), residues: 1444 helix: -4.06 (0.06), residues: 1254 sheet: None (None), residues: 0 loop : -4.86 (0.27), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG U 58 TYR 0.010 0.002 TYR D 57 PHE 0.020 0.004 PHE U 68 TRP 0.016 0.004 TRP G 5 Details of bonding type rmsd covalent geometry : bond 0.00794 (11837) covalent geometry : angle 0.75247 (16112) hydrogen bonds : bond 0.26261 ( 893) hydrogen bonds : angle 9.46006 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ASP cc_start: 0.7305 (m-30) cc_final: 0.7001 (m-30) REVERT: D 12 VAL cc_start: 0.9496 (t) cc_final: 0.9264 (t) REVERT: D 26 GLN cc_start: 0.7390 (mt0) cc_final: 0.7068 (mt0) REVERT: D 33 LYS cc_start: 0.8263 (mttt) cc_final: 0.7696 (mmtt) REVERT: D 54 TYR cc_start: 0.8293 (t80) cc_final: 0.8030 (t80) REVERT: U 15 LYS cc_start: 0.8811 (mttt) cc_final: 0.8489 (mmmm) REVERT: U 25 THR cc_start: 0.8574 (m) cc_final: 0.8034 (p) REVERT: U 28 THR cc_start: 0.8521 (m) cc_final: 0.8288 (p) REVERT: U 37 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7199 (tptt) REVERT: U 43 LEU cc_start: 0.9411 (mt) cc_final: 0.8678 (mt) REVERT: U 53 GLU cc_start: 0.8675 (tp30) cc_final: 0.8447 (tp30) REVERT: U 66 LYS cc_start: 0.8544 (tptp) cc_final: 0.7281 (mttt) REVERT: V 28 THR cc_start: 0.8981 (m) cc_final: 0.8129 (p) REVERT: V 33 LYS cc_start: 0.8265 (mttt) cc_final: 0.7498 (mtmt) REVERT: V 37 LYS cc_start: 0.9168 (ttmt) cc_final: 0.7889 (tptt) REVERT: V 47 TYR cc_start: 0.9134 (t80) cc_final: 0.8045 (t80) REVERT: V 53 GLU cc_start: 0.8174 (tp30) cc_final: 0.7797 (tp30) REVERT: E 28 THR cc_start: 0.7588 (m) cc_final: 0.7083 (p) REVERT: E 32 ASP cc_start: 0.7929 (m-30) cc_final: 0.7719 (m-30) REVERT: E 37 LYS cc_start: 0.7405 (ttmt) cc_final: 0.6675 (tptt) REVERT: F 28 THR cc_start: 0.9130 (m) cc_final: 0.8353 (p) REVERT: F 34 LEU cc_start: 0.9349 (tp) cc_final: 0.9101 (tt) REVERT: F 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7915 (tptt) REVERT: F 39 SER cc_start: 0.9258 (m) cc_final: 0.8971 (t) REVERT: F 47 TYR cc_start: 0.9116 (t80) cc_final: 0.8106 (t80) REVERT: F 49 SER cc_start: 0.8330 (t) cc_final: 0.8086 (p) REVERT: F 63 ASN cc_start: 0.8789 (m-40) cc_final: 0.8179 (m-40) REVERT: F 66 LYS cc_start: 0.8562 (tptp) cc_final: 0.7286 (mttm) REVERT: G 8 TYR cc_start: 0.8726 (t80) cc_final: 0.8493 (t80) REVERT: G 11 ASP cc_start: 0.8244 (m-30) cc_final: 0.7717 (m-30) REVERT: G 23 LEU cc_start: 0.8811 (tp) cc_final: 0.8543 (tp) REVERT: G 37 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7112 (tptt) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.8165 (t80) REVERT: H 22 ASN cc_start: 0.8247 (p0) cc_final: 0.7969 (p0) REVERT: H 28 THR cc_start: 0.9268 (m) cc_final: 0.8613 (p) REVERT: H 32 ASP cc_start: 0.8001 (m-30) cc_final: 0.7663 (m-30) REVERT: H 37 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7180 (tptt) REVERT: H 39 SER cc_start: 0.9287 (m) cc_final: 0.8695 (m) REVERT: I 28 THR cc_start: 0.9439 (m) cc_final: 0.9119 (m) REVERT: I 31 LEU cc_start: 0.9475 (tp) cc_final: 0.9100 (tp) REVERT: I 32 ASP cc_start: 0.8545 (m-30) cc_final: 0.8199 (m-30) REVERT: I 37 LYS cc_start: 0.8662 (ttmt) cc_final: 0.7393 (tptt) REVERT: I 47 TYR cc_start: 0.9254 (t80) cc_final: 0.8950 (t80) REVERT: I 49 SER cc_start: 0.9083 (t) cc_final: 0.8777 (t) REVERT: J 6 SER cc_start: 0.8989 (m) cc_final: 0.8767 (p) REVERT: J 24 GLN cc_start: 0.7828 (mp10) cc_final: 0.7618 (tp-100) REVERT: J 37 LYS cc_start: 0.8754 (ttmt) cc_final: 0.7267 (tptt) REVERT: J 47 TYR cc_start: 0.9064 (t80) cc_final: 0.8457 (t80) REVERT: J 49 SER cc_start: 0.9100 (t) cc_final: 0.8862 (t) REVERT: J 51 LEU cc_start: 0.8744 (tp) cc_final: 0.8259 (tt) REVERT: J 54 TYR cc_start: 0.8899 (t80) cc_final: 0.8495 (t80) REVERT: J 57 TYR cc_start: 0.8689 (t80) cc_final: 0.8452 (t80) REVERT: J 58 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7880 (mmt180) REVERT: J 64 THR cc_start: 0.8630 (m) cc_final: 0.8232 (m) REVERT: K 9 LEU cc_start: 0.9230 (mt) cc_final: 0.8980 (mm) REVERT: K 37 LYS cc_start: 0.9113 (ttmt) cc_final: 0.7915 (tptp) REVERT: K 39 SER cc_start: 0.8861 (m) cc_final: 0.8641 (t) REVERT: K 47 TYR cc_start: 0.9029 (t80) cc_final: 0.8022 (t80) REVERT: K 54 TYR cc_start: 0.8955 (t80) cc_final: 0.8625 (t80) REVERT: K 61 GLN cc_start: 0.8940 (tt0) cc_final: 0.8709 (tt0) REVERT: L 23 LEU cc_start: 0.8841 (tp) cc_final: 0.8296 (tt) REVERT: L 26 GLN cc_start: 0.8671 (mt0) cc_final: 0.8421 (mt0) REVERT: L 37 LYS cc_start: 0.9006 (ttmt) cc_final: 0.7242 (tptt) REVERT: L 39 SER cc_start: 0.9050 (m) cc_final: 0.8790 (t) REVERT: L 53 GLU cc_start: 0.8349 (tp30) cc_final: 0.7778 (tp30) REVERT: M 28 THR cc_start: 0.9247 (m) cc_final: 0.8055 (p) REVERT: M 31 LEU cc_start: 0.9203 (tp) cc_final: 0.8779 (tt) REVERT: M 33 LYS cc_start: 0.9116 (mttt) cc_final: 0.8861 (mtmt) REVERT: M 39 SER cc_start: 0.9295 (m) cc_final: 0.8820 (p) REVERT: M 47 TYR cc_start: 0.9139 (t80) cc_final: 0.8714 (t80) REVERT: M 51 LEU cc_start: 0.9386 (tp) cc_final: 0.9087 (tp) REVERT: M 54 TYR cc_start: 0.9097 (t80) cc_final: 0.8802 (t80) REVERT: N 31 LEU cc_start: 0.9170 (tp) cc_final: 0.8866 (tt) REVERT: N 43 LEU cc_start: 0.9280 (mt) cc_final: 0.8978 (mt) REVERT: N 47 TYR cc_start: 0.9145 (t80) cc_final: 0.8639 (t80) REVERT: N 51 LEU cc_start: 0.9065 (tp) cc_final: 0.8667 (tt) REVERT: N 58 ARG cc_start: 0.8693 (mmt180) cc_final: 0.8489 (mmt180) REVERT: O 9 LEU cc_start: 0.9010 (mt) cc_final: 0.8703 (mt) REVERT: O 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8674 (tppt) REVERT: O 17 ASP cc_start: 0.7785 (m-30) cc_final: 0.7428 (t0) REVERT: O 22 ASN cc_start: 0.9063 (p0) cc_final: 0.7894 (p0) REVERT: O 25 THR cc_start: 0.8817 (m) cc_final: 0.8391 (m) REVERT: O 28 THR cc_start: 0.8657 (m) cc_final: 0.8344 (p) REVERT: O 33 LYS cc_start: 0.9062 (mttt) cc_final: 0.8847 (mmmm) REVERT: O 47 TYR cc_start: 0.8941 (t80) cc_final: 0.8642 (t80) REVERT: O 50 LYS cc_start: 0.9063 (mmtt) cc_final: 0.8833 (mmtm) REVERT: O 53 GLU cc_start: 0.8604 (tp30) cc_final: 0.8305 (tp30) REVERT: O 55 ASN cc_start: 0.9010 (t0) cc_final: 0.7921 (t0) REVERT: O 58 ARG cc_start: 0.8940 (mmt180) cc_final: 0.8616 (mmt-90) REVERT: O 59 ASN cc_start: 0.8739 (m-40) cc_final: 0.8134 (m110) REVERT: O 69 LYS cc_start: 0.8210 (tttm) cc_final: 0.7947 (tptt) REVERT: P 22 ASN cc_start: 0.9054 (p0) cc_final: 0.8649 (p0) REVERT: P 40 ASP cc_start: 0.7928 (t0) cc_final: 0.7706 (t0) REVERT: P 56 LEU cc_start: 0.9466 (mt) cc_final: 0.8965 (mp) REVERT: Q 33 LYS cc_start: 0.8819 (mttt) cc_final: 0.8523 (mttp) REVERT: Q 47 TYR cc_start: 0.9157 (t80) cc_final: 0.8888 (t80) REVERT: Q 51 LEU cc_start: 0.9225 (tp) cc_final: 0.8827 (tp) REVERT: Q 56 LEU cc_start: 0.9501 (mt) cc_final: 0.9244 (mm) REVERT: Q 57 TYR cc_start: 0.9030 (t80) cc_final: 0.8534 (t80) REVERT: Q 58 ARG cc_start: 0.8919 (mmt180) cc_final: 0.8668 (mmt-90) REVERT: Q 69 LYS cc_start: 0.8488 (tttm) cc_final: 0.7626 (tptt) REVERT: R 6 SER cc_start: 0.8532 (m) cc_final: 0.8202 (t) REVERT: R 22 ASN cc_start: 0.8994 (p0) cc_final: 0.7796 (p0) REVERT: R 25 THR cc_start: 0.8501 (m) cc_final: 0.7823 (p) REVERT: R 28 THR cc_start: 0.8689 (m) cc_final: 0.8055 (p) REVERT: R 39 SER cc_start: 0.9221 (m) cc_final: 0.8748 (t) REVERT: R 56 LEU cc_start: 0.9130 (mt) cc_final: 0.8747 (mt) REVERT: S 22 ASN cc_start: 0.8719 (p0) cc_final: 0.8455 (p0) REVERT: S 25 THR cc_start: 0.7755 (m) cc_final: 0.6977 (p) REVERT: S 31 LEU cc_start: 0.8716 (tp) cc_final: 0.8108 (tp) REVERT: S 33 LYS cc_start: 0.8394 (mttt) cc_final: 0.8104 (ttmm) REVERT: T 22 ASN cc_start: 0.8787 (p0) cc_final: 0.8096 (p0) REVERT: T 25 THR cc_start: 0.8429 (m) cc_final: 0.7695 (p) REVERT: T 26 GLN cc_start: 0.9243 (mt0) cc_final: 0.8906 (mt0) REVERT: T 28 THR cc_start: 0.8064 (m) cc_final: 0.7510 (p) REVERT: T 39 SER cc_start: 0.9144 (m) cc_final: 0.8937 (p) REVERT: T 43 LEU cc_start: 0.9287 (mt) cc_final: 0.8440 (mt) REVERT: T 47 TYR cc_start: 0.9026 (t80) cc_final: 0.8042 (t80) REVERT: T 50 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8752 (mmtt) REVERT: T 57 TYR cc_start: 0.8561 (t80) cc_final: 0.7517 (t80) REVERT: T 58 ARG cc_start: 0.8754 (mmt180) cc_final: 0.6825 (mtt180) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.0963 time to fit residues: 87.5307 Evaluate side-chains 527 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN U 26 GLN F 77 GLN G 78 ASN I 63 ASN J 26 GLN K 63 ASN L 63 ASN M 61 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN R 63 ASN S 48 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105691 restraints weight = 17251.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109107 restraints weight = 8782.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111404 restraints weight = 5549.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112971 restraints weight = 4011.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113964 restraints weight = 3158.316| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11837 Z= 0.153 Angle : 0.551 5.637 16112 Z= 0.304 Chirality : 0.037 0.128 1843 Planarity : 0.004 0.023 2109 Dihedral : 4.210 15.247 1596 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.95 % Allowed : 11.32 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.18), residues: 1444 helix: -0.75 (0.12), residues: 1292 sheet: None (None), residues: 0 loop : -5.28 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 80 TYR 0.017 0.002 TYR O 54 PHE 0.010 0.001 PHE T 79 TRP 0.028 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00321 (11837) covalent geometry : angle 0.55056 (16112) hydrogen bonds : bond 0.04629 ( 893) hydrogen bonds : angle 3.37013 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 582 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8546 (mmmm) cc_final: 0.8200 (mmmt) REVERT: U 15 LYS cc_start: 0.8926 (mttt) cc_final: 0.8451 (mmmm) REVERT: U 37 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7194 (tptp) REVERT: U 53 GLU cc_start: 0.8399 (tp30) cc_final: 0.8042 (mm-30) REVERT: U 66 LYS cc_start: 0.8735 (tptp) cc_final: 0.6626 (mttt) REVERT: V 28 THR cc_start: 0.8729 (m) cc_final: 0.8308 (p) REVERT: V 37 LYS cc_start: 0.9249 (ttmt) cc_final: 0.7914 (tptt) REVERT: V 47 TYR cc_start: 0.8975 (t80) cc_final: 0.8205 (t80) REVERT: V 49 SER cc_start: 0.8627 (t) cc_final: 0.8269 (p) REVERT: V 53 GLU cc_start: 0.8408 (tp30) cc_final: 0.7974 (mm-30) REVERT: V 77 GLN cc_start: 0.8337 (tp40) cc_final: 0.7738 (tp-100) REVERT: E 32 ASP cc_start: 0.8073 (m-30) cc_final: 0.7839 (m-30) REVERT: E 37 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7052 (tptt) REVERT: E 48 GLN cc_start: 0.8852 (tm-30) cc_final: 0.8578 (tm-30) REVERT: E 57 TYR cc_start: 0.8386 (t80) cc_final: 0.7888 (t80) REVERT: F 28 THR cc_start: 0.8726 (m) cc_final: 0.8220 (p) REVERT: F 32 ASP cc_start: 0.7691 (m-30) cc_final: 0.7417 (m-30) REVERT: F 34 LEU cc_start: 0.9251 (tp) cc_final: 0.8991 (tt) REVERT: F 37 LYS cc_start: 0.8610 (ttmt) cc_final: 0.7927 (tptt) REVERT: F 39 SER cc_start: 0.8689 (m) cc_final: 0.8290 (t) REVERT: F 47 TYR cc_start: 0.8908 (t80) cc_final: 0.8167 (t80) REVERT: F 49 SER cc_start: 0.9228 (t) cc_final: 0.8823 (p) REVERT: F 53 GLU cc_start: 0.8411 (tp30) cc_final: 0.7507 (mm-30) REVERT: F 66 LYS cc_start: 0.8836 (tptp) cc_final: 0.7260 (mttm) REVERT: G 11 ASP cc_start: 0.8373 (m-30) cc_final: 0.7833 (m-30) REVERT: G 15 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8873 (ttmm) REVERT: G 37 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7177 (tptt) REVERT: G 49 SER cc_start: 0.8748 (t) cc_final: 0.8195 (m) REVERT: G 69 LYS cc_start: 0.8548 (tttm) cc_final: 0.8309 (tttt) REVERT: H 28 THR cc_start: 0.8999 (m) cc_final: 0.8466 (p) REVERT: H 31 LEU cc_start: 0.8875 (tp) cc_final: 0.8601 (tt) REVERT: H 32 ASP cc_start: 0.8020 (m-30) cc_final: 0.7564 (m-30) REVERT: H 37 LYS cc_start: 0.8111 (ttmt) cc_final: 0.6945 (tptt) REVERT: H 39 SER cc_start: 0.9130 (m) cc_final: 0.8903 (m) REVERT: H 47 TYR cc_start: 0.9150 (t80) cc_final: 0.7443 (t80) REVERT: H 51 LEU cc_start: 0.9241 (tp) cc_final: 0.8781 (tp) REVERT: I 28 THR cc_start: 0.9030 (m) cc_final: 0.8697 (p) REVERT: I 32 ASP cc_start: 0.8536 (m-30) cc_final: 0.8266 (m-30) REVERT: I 37 LYS cc_start: 0.8716 (ttmt) cc_final: 0.7315 (tptp) REVERT: I 47 TYR cc_start: 0.9261 (t80) cc_final: 0.8948 (t80) REVERT: I 49 SER cc_start: 0.9123 (t) cc_final: 0.8919 (t) REVERT: J 24 GLN cc_start: 0.8208 (mp10) cc_final: 0.7824 (tp-100) REVERT: J 37 LYS cc_start: 0.8776 (ttmt) cc_final: 0.7293 (tptp) REVERT: J 47 TYR cc_start: 0.9239 (t80) cc_final: 0.8688 (t80) REVERT: J 49 SER cc_start: 0.9268 (t) cc_final: 0.8796 (p) REVERT: J 50 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8663 (mmtt) REVERT: J 69 LYS cc_start: 0.8409 (tttm) cc_final: 0.8195 (tmtt) REVERT: K 37 LYS cc_start: 0.9101 (ttmt) cc_final: 0.7777 (tptt) REVERT: K 40 ASP cc_start: 0.8053 (t0) cc_final: 0.7801 (t70) REVERT: K 47 TYR cc_start: 0.9139 (t80) cc_final: 0.8180 (t80) REVERT: K 50 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8829 (mmtp) REVERT: K 77 GLN cc_start: 0.8528 (tp40) cc_final: 0.8307 (tp-100) REVERT: L 23 LEU cc_start: 0.8810 (tp) cc_final: 0.8345 (tt) REVERT: L 26 GLN cc_start: 0.8530 (mt0) cc_final: 0.8287 (mt0) REVERT: L 31 LEU cc_start: 0.9156 (tp) cc_final: 0.8913 (tp) REVERT: L 37 LYS cc_start: 0.8748 (ttmt) cc_final: 0.7152 (tptt) REVERT: L 53 GLU cc_start: 0.8233 (tp30) cc_final: 0.7891 (tp30) REVERT: M 28 THR cc_start: 0.8750 (m) cc_final: 0.8318 (p) REVERT: M 31 LEU cc_start: 0.9145 (tp) cc_final: 0.8706 (tt) REVERT: M 32 ASP cc_start: 0.8380 (p0) cc_final: 0.8154 (p0) REVERT: M 39 SER cc_start: 0.9179 (m) cc_final: 0.8800 (p) REVERT: M 47 TYR cc_start: 0.9091 (t80) cc_final: 0.8572 (t80) REVERT: M 50 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8829 (mmtt) REVERT: M 66 LYS cc_start: 0.8730 (tptt) cc_final: 0.8132 (tmtt) REVERT: N 43 LEU cc_start: 0.9182 (mt) cc_final: 0.8876 (mp) REVERT: N 47 TYR cc_start: 0.8958 (t80) cc_final: 0.8543 (t80) REVERT: N 49 SER cc_start: 0.9600 (m) cc_final: 0.9344 (t) REVERT: N 50 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8735 (mmmt) REVERT: N 51 LEU cc_start: 0.9017 (tp) cc_final: 0.8768 (tt) REVERT: N 53 GLU cc_start: 0.8208 (tp30) cc_final: 0.7693 (tp30) REVERT: N 58 ARG cc_start: 0.8389 (mmt180) cc_final: 0.8142 (mmt180) REVERT: O 17 ASP cc_start: 0.7908 (m-30) cc_final: 0.7136 (t0) REVERT: O 22 ASN cc_start: 0.9201 (p0) cc_final: 0.8376 (p0) REVERT: O 25 THR cc_start: 0.9057 (m) cc_final: 0.8722 (m) REVERT: O 28 THR cc_start: 0.8615 (m) cc_final: 0.7275 (p) REVERT: O 33 LYS cc_start: 0.9142 (mttt) cc_final: 0.8462 (mtmm) REVERT: O 49 SER cc_start: 0.9454 (m) cc_final: 0.9150 (t) REVERT: O 58 ARG cc_start: 0.8629 (mmt180) cc_final: 0.8338 (mmt-90) REVERT: O 59 ASN cc_start: 0.8537 (m-40) cc_final: 0.7800 (m110) REVERT: O 69 LYS cc_start: 0.8367 (tttm) cc_final: 0.7808 (tttt) REVERT: P 22 ASN cc_start: 0.9147 (p0) cc_final: 0.8867 (p0) REVERT: Q 28 THR cc_start: 0.8237 (m) cc_final: 0.7998 (p) REVERT: Q 40 ASP cc_start: 0.8341 (t0) cc_final: 0.7884 (t0) REVERT: Q 54 TYR cc_start: 0.8427 (t80) cc_final: 0.7849 (t80) REVERT: Q 57 TYR cc_start: 0.8987 (t80) cc_final: 0.8523 (t80) REVERT: Q 69 LYS cc_start: 0.8555 (tttm) cc_final: 0.8104 (ttmt) REVERT: Q 76 ILE cc_start: 0.8113 (mm) cc_final: 0.7848 (tt) REVERT: R 22 ASN cc_start: 0.8909 (p0) cc_final: 0.8169 (p0) REVERT: R 24 GLN cc_start: 0.8293 (mp10) cc_final: 0.8045 (pm20) REVERT: R 25 THR cc_start: 0.8605 (m) cc_final: 0.8096 (p) REVERT: R 29 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8033 (tm-30) REVERT: R 33 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8523 (mtmt) REVERT: S 25 THR cc_start: 0.8161 (m) cc_final: 0.7823 (p) REVERT: S 39 SER cc_start: 0.8938 (m) cc_final: 0.8067 (m) REVERT: T 22 ASN cc_start: 0.8585 (p0) cc_final: 0.8056 (p0) REVERT: T 26 GLN cc_start: 0.9151 (mt0) cc_final: 0.8947 (mt0) REVERT: T 31 LEU cc_start: 0.8891 (tp) cc_final: 0.8639 (tp) REVERT: T 39 SER cc_start: 0.9084 (m) cc_final: 0.8735 (p) REVERT: T 40 ASP cc_start: 0.8302 (t0) cc_final: 0.7929 (t0) REVERT: T 48 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8811 (tm-30) REVERT: T 50 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8712 (mmmt) REVERT: T 66 LYS cc_start: 0.9016 (tptp) cc_final: 0.8665 (tppt) REVERT: T 69 LYS cc_start: 0.7015 (tttm) cc_final: 0.6628 (ttmt) outliers start: 37 outliers final: 25 residues processed: 595 average time/residue: 0.0901 time to fit residues: 76.2522 Evaluate side-chains 562 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 536 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 39 SER Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 10 ASP Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN U 26 GLN K 24 GLN M 26 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 GLN S 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101424 restraints weight = 17602.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104687 restraints weight = 9234.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.106817 restraints weight = 5936.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108381 restraints weight = 4370.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109413 restraints weight = 3471.979| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11837 Z= 0.160 Angle : 0.515 7.549 16112 Z= 0.274 Chirality : 0.038 0.110 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.887 18.206 1596 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.07 % Allowed : 15.39 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.21), residues: 1444 helix: 0.74 (0.13), residues: 1292 sheet: None (None), residues: 0 loop : -5.06 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 80 TYR 0.019 0.002 TYR N 57 PHE 0.008 0.001 PHE T 79 TRP 0.014 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00349 (11837) covalent geometry : angle 0.51540 (16112) hydrogen bonds : bond 0.03987 ( 893) hydrogen bonds : angle 3.08202 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 564 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8382 (mmmt) REVERT: D 22 ASN cc_start: 0.7408 (p0) cc_final: 0.7172 (p0) REVERT: D 23 LEU cc_start: 0.7750 (tt) cc_final: 0.7530 (tt) REVERT: U 15 LYS cc_start: 0.8992 (mttt) cc_final: 0.8474 (mmmm) REVERT: U 37 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7291 (tptp) REVERT: U 66 LYS cc_start: 0.8664 (tptp) cc_final: 0.7027 (mttt) REVERT: V 37 LYS cc_start: 0.9170 (ttmt) cc_final: 0.7759 (tptt) REVERT: V 47 TYR cc_start: 0.9056 (t80) cc_final: 0.8359 (t80) REVERT: V 49 SER cc_start: 0.8608 (t) cc_final: 0.8246 (p) REVERT: V 53 GLU cc_start: 0.8077 (tp30) cc_final: 0.7863 (mm-30) REVERT: V 77 GLN cc_start: 0.8616 (tp40) cc_final: 0.7943 (tp-100) REVERT: E 11 ASP cc_start: 0.8244 (m-30) cc_final: 0.7782 (m-30) REVERT: E 37 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7318 (tptt) REVERT: E 54 TYR cc_start: 0.8698 (t80) cc_final: 0.8419 (t80) REVERT: E 66 LYS cc_start: 0.8070 (tptp) cc_final: 0.6174 (mttt) REVERT: E 69 LYS cc_start: 0.7972 (tttm) cc_final: 0.7696 (tptp) REVERT: E 72 ASP cc_start: 0.8581 (m-30) cc_final: 0.8360 (t0) REVERT: F 28 THR cc_start: 0.8711 (m) cc_final: 0.8129 (p) REVERT: F 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7460 (m-30) REVERT: F 34 LEU cc_start: 0.9235 (tp) cc_final: 0.8956 (tt) REVERT: F 37 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7748 (tptt) REVERT: F 39 SER cc_start: 0.8771 (m) cc_final: 0.8220 (t) REVERT: F 47 TYR cc_start: 0.8893 (t80) cc_final: 0.8245 (t80) REVERT: F 49 SER cc_start: 0.9293 (t) cc_final: 0.8980 (p) REVERT: F 53 GLU cc_start: 0.8348 (tp30) cc_final: 0.7786 (mm-30) REVERT: F 66 LYS cc_start: 0.8816 (tptp) cc_final: 0.7322 (mttm) REVERT: G 11 ASP cc_start: 0.8385 (m-30) cc_final: 0.7961 (t0) REVERT: G 15 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8738 (ttmm) REVERT: G 37 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7134 (tptt) REVERT: G 69 LYS cc_start: 0.8727 (tttm) cc_final: 0.8385 (tttt) REVERT: H 23 LEU cc_start: 0.8874 (tp) cc_final: 0.8639 (tt) REVERT: H 28 THR cc_start: 0.8956 (m) cc_final: 0.8340 (p) REVERT: H 31 LEU cc_start: 0.8806 (tp) cc_final: 0.8587 (tt) REVERT: H 32 ASP cc_start: 0.7776 (m-30) cc_final: 0.7343 (m-30) REVERT: H 37 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7003 (tptt) REVERT: H 47 TYR cc_start: 0.9143 (t80) cc_final: 0.7367 (t80) REVERT: H 51 LEU cc_start: 0.9313 (tp) cc_final: 0.8777 (tp) REVERT: H 77 GLN cc_start: 0.8565 (tp40) cc_final: 0.8354 (tp40) REVERT: I 28 THR cc_start: 0.9051 (m) cc_final: 0.8722 (p) REVERT: I 32 ASP cc_start: 0.8437 (m-30) cc_final: 0.8184 (m-30) REVERT: I 37 LYS cc_start: 0.8696 (ttmt) cc_final: 0.7314 (tptp) REVERT: I 47 TYR cc_start: 0.9276 (t80) cc_final: 0.8923 (t80) REVERT: I 49 SER cc_start: 0.9082 (t) cc_final: 0.8863 (t) REVERT: J 17 ASP cc_start: 0.7962 (m-30) cc_final: 0.7673 (m-30) REVERT: J 22 ASN cc_start: 0.8108 (p0) cc_final: 0.7515 (p0) REVERT: J 24 GLN cc_start: 0.7934 (mp10) cc_final: 0.7667 (tp-100) REVERT: J 37 LYS cc_start: 0.8777 (ttmt) cc_final: 0.7333 (tptt) REVERT: J 47 TYR cc_start: 0.9188 (t80) cc_final: 0.8630 (t80) REVERT: J 49 SER cc_start: 0.9241 (t) cc_final: 0.8860 (p) REVERT: K 33 LYS cc_start: 0.9193 (mttt) cc_final: 0.8813 (mtpp) REVERT: K 37 LYS cc_start: 0.9119 (ttmt) cc_final: 0.7762 (tptt) REVERT: K 47 TYR cc_start: 0.9141 (t80) cc_final: 0.7808 (t80) REVERT: K 63 ASN cc_start: 0.8606 (m-40) cc_final: 0.8337 (m110) REVERT: L 23 LEU cc_start: 0.8597 (tp) cc_final: 0.8279 (tt) REVERT: L 26 GLN cc_start: 0.8623 (mt0) cc_final: 0.8413 (tt0) REVERT: L 37 LYS cc_start: 0.8730 (ttmt) cc_final: 0.6977 (tptt) REVERT: L 48 GLN cc_start: 0.8579 (tt0) cc_final: 0.7966 (tt0) REVERT: L 53 GLU cc_start: 0.8135 (tp30) cc_final: 0.7840 (tp30) REVERT: M 28 THR cc_start: 0.8822 (m) cc_final: 0.8246 (p) REVERT: M 31 LEU cc_start: 0.9261 (tp) cc_final: 0.8762 (tt) REVERT: M 32 ASP cc_start: 0.8389 (p0) cc_final: 0.8112 (p0) REVERT: M 33 LYS cc_start: 0.9121 (mttt) cc_final: 0.8877 (mtpt) REVERT: M 39 SER cc_start: 0.9260 (m) cc_final: 0.9048 (p) REVERT: M 47 TYR cc_start: 0.9228 (t80) cc_final: 0.8618 (t80) REVERT: M 66 LYS cc_start: 0.8800 (tptt) cc_final: 0.8117 (tmtt) REVERT: N 15 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8249 (ttmm) REVERT: N 24 GLN cc_start: 0.8768 (mp10) cc_final: 0.8125 (tm-30) REVERT: N 32 ASP cc_start: 0.8178 (m-30) cc_final: 0.7951 (m-30) REVERT: N 47 TYR cc_start: 0.8878 (t80) cc_final: 0.8573 (t80) REVERT: N 49 SER cc_start: 0.9526 (m) cc_final: 0.9274 (t) REVERT: N 50 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8512 (mmmt) REVERT: N 51 LEU cc_start: 0.9017 (tp) cc_final: 0.8713 (tt) REVERT: N 53 GLU cc_start: 0.8225 (tp30) cc_final: 0.7669 (tp30) REVERT: O 17 ASP cc_start: 0.7906 (m-30) cc_final: 0.7249 (t0) REVERT: O 22 ASN cc_start: 0.9224 (p0) cc_final: 0.7769 (p0) REVERT: O 25 THR cc_start: 0.9077 (m) cc_final: 0.8396 (p) REVERT: O 28 THR cc_start: 0.8500 (m) cc_final: 0.8173 (p) REVERT: O 33 LYS cc_start: 0.9131 (mttt) cc_final: 0.8438 (mtmm) REVERT: O 49 SER cc_start: 0.9313 (m) cc_final: 0.8976 (t) REVERT: O 50 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8834 (mmpt) REVERT: O 52 SER cc_start: 0.9024 (m) cc_final: 0.8774 (t) REVERT: O 59 ASN cc_start: 0.8632 (m-40) cc_final: 0.7873 (m110) REVERT: O 69 LYS cc_start: 0.8100 (tttm) cc_final: 0.7810 (ttmt) REVERT: O 77 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8387 (tp-100) REVERT: P 22 ASN cc_start: 0.9207 (p0) cc_final: 0.8718 (p0) REVERT: P 24 GLN cc_start: 0.8183 (mp10) cc_final: 0.7958 (mp10) REVERT: P 26 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8927 (tt0) REVERT: P 56 LEU cc_start: 0.9305 (mt) cc_final: 0.9088 (mp) REVERT: Q 17 ASP cc_start: 0.7728 (m-30) cc_final: 0.7426 (m-30) REVERT: Q 25 THR cc_start: 0.8776 (m) cc_final: 0.8319 (p) REVERT: Q 28 THR cc_start: 0.8247 (m) cc_final: 0.7991 (p) REVERT: Q 40 ASP cc_start: 0.8230 (t0) cc_final: 0.7667 (t0) REVERT: Q 54 TYR cc_start: 0.8476 (t80) cc_final: 0.8022 (t80) REVERT: Q 57 TYR cc_start: 0.8903 (t80) cc_final: 0.8457 (t80) REVERT: Q 69 LYS cc_start: 0.8572 (tttm) cc_final: 0.8073 (ttmt) REVERT: R 22 ASN cc_start: 0.8917 (p0) cc_final: 0.8220 (p0) REVERT: R 24 GLN cc_start: 0.8291 (mp10) cc_final: 0.8084 (pm20) REVERT: R 33 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8658 (mtmt) REVERT: S 25 THR cc_start: 0.8086 (m) cc_final: 0.7837 (p) REVERT: S 39 SER cc_start: 0.9170 (m) cc_final: 0.8276 (m) REVERT: S 59 ASN cc_start: 0.8684 (m-40) cc_final: 0.8058 (m110) REVERT: T 22 ASN cc_start: 0.8434 (p0) cc_final: 0.8210 (p0) REVERT: T 25 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8147 (t) REVERT: T 39 SER cc_start: 0.9031 (m) cc_final: 0.8647 (p) REVERT: T 48 GLN cc_start: 0.9029 (tm-30) cc_final: 0.8810 (tm-30) REVERT: T 50 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8743 (mmmt) REVERT: T 69 LYS cc_start: 0.7095 (tttm) cc_final: 0.6583 (ttmt) outliers start: 51 outliers final: 33 residues processed: 578 average time/residue: 0.0885 time to fit residues: 73.3001 Evaluate side-chains 573 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 538 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 26 GLN Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN R 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097878 restraints weight = 17744.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101066 restraints weight = 9367.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103174 restraints weight = 6072.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104714 restraints weight = 4483.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105748 restraints weight = 3568.237| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11837 Z= 0.179 Angle : 0.522 6.968 16112 Z= 0.275 Chirality : 0.039 0.111 1843 Planarity : 0.003 0.016 2109 Dihedral : 3.834 20.986 1596 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.07 % Allowed : 18.58 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1444 helix: 1.36 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.87 (0.28), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 58 TYR 0.013 0.002 TYR G 57 PHE 0.010 0.001 PHE N 68 TRP 0.009 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00407 (11837) covalent geometry : angle 0.52185 (16112) hydrogen bonds : bond 0.03627 ( 893) hydrogen bonds : angle 3.02960 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 569 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8846 (mmmm) cc_final: 0.8474 (mmmt) REVERT: D 22 ASN cc_start: 0.7812 (p0) cc_final: 0.7312 (p0) REVERT: D 23 LEU cc_start: 0.7837 (tt) cc_final: 0.7402 (tt) REVERT: U 15 LYS cc_start: 0.9067 (mttt) cc_final: 0.8710 (mmtp) REVERT: U 37 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7222 (tptp) REVERT: U 66 LYS cc_start: 0.8652 (tptp) cc_final: 0.7002 (mttt) REVERT: V 37 LYS cc_start: 0.8710 (ttmt) cc_final: 0.7502 (tptt) REVERT: V 47 TYR cc_start: 0.9140 (t80) cc_final: 0.8327 (t80) REVERT: V 49 SER cc_start: 0.8619 (t) cc_final: 0.8233 (p) REVERT: V 51 LEU cc_start: 0.9150 (tp) cc_final: 0.8930 (tp) REVERT: V 77 GLN cc_start: 0.8729 (tp40) cc_final: 0.8021 (tp-100) REVERT: E 15 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8502 (mmmt) REVERT: E 23 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7285 (tp) REVERT: E 37 LYS cc_start: 0.8600 (ttmt) cc_final: 0.7373 (tptp) REVERT: E 47 TYR cc_start: 0.8914 (t80) cc_final: 0.8631 (t80) REVERT: E 53 GLU cc_start: 0.8784 (tp30) cc_final: 0.8200 (mm-30) REVERT: E 66 LYS cc_start: 0.8283 (tptp) cc_final: 0.6799 (mttt) REVERT: F 28 THR cc_start: 0.8727 (m) cc_final: 0.8115 (p) REVERT: F 32 ASP cc_start: 0.7762 (m-30) cc_final: 0.7424 (m-30) REVERT: F 34 LEU cc_start: 0.9234 (tp) cc_final: 0.8968 (tt) REVERT: F 37 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7831 (tptt) REVERT: F 39 SER cc_start: 0.8868 (m) cc_final: 0.8222 (t) REVERT: F 47 TYR cc_start: 0.8962 (t80) cc_final: 0.8343 (t80) REVERT: F 49 SER cc_start: 0.9273 (t) cc_final: 0.8889 (p) REVERT: F 53 GLU cc_start: 0.8331 (tp30) cc_final: 0.7734 (mm-30) REVERT: F 63 ASN cc_start: 0.9188 (m-40) cc_final: 0.8978 (m110) REVERT: F 66 LYS cc_start: 0.8656 (tptp) cc_final: 0.7328 (mttm) REVERT: G 11 ASP cc_start: 0.8232 (m-30) cc_final: 0.7947 (t0) REVERT: G 15 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8806 (ttmm) REVERT: G 37 LYS cc_start: 0.8517 (ttmt) cc_final: 0.7217 (tptt) REVERT: G 69 LYS cc_start: 0.8745 (tttm) cc_final: 0.8423 (tttt) REVERT: H 28 THR cc_start: 0.8978 (m) cc_final: 0.8317 (p) REVERT: H 32 ASP cc_start: 0.7818 (m-30) cc_final: 0.7470 (m-30) REVERT: H 37 LYS cc_start: 0.8182 (ttmt) cc_final: 0.6890 (tptt) REVERT: H 47 TYR cc_start: 0.9136 (t80) cc_final: 0.7375 (t80) REVERT: H 51 LEU cc_start: 0.9354 (tp) cc_final: 0.8752 (tp) REVERT: H 77 GLN cc_start: 0.8590 (tp40) cc_final: 0.8390 (tp40) REVERT: I 28 THR cc_start: 0.9062 (m) cc_final: 0.8722 (p) REVERT: I 32 ASP cc_start: 0.8416 (m-30) cc_final: 0.8189 (m-30) REVERT: I 37 LYS cc_start: 0.8729 (ttmt) cc_final: 0.7376 (tptp) REVERT: I 47 TYR cc_start: 0.9280 (t80) cc_final: 0.8948 (t80) REVERT: I 49 SER cc_start: 0.8998 (t) cc_final: 0.8782 (t) REVERT: I 77 GLN cc_start: 0.8594 (tp40) cc_final: 0.8377 (tp40) REVERT: J 17 ASP cc_start: 0.7974 (m-30) cc_final: 0.7729 (m-30) REVERT: J 22 ASN cc_start: 0.8147 (p0) cc_final: 0.7605 (p0) REVERT: J 37 LYS cc_start: 0.8801 (ttmt) cc_final: 0.7336 (tptt) REVERT: J 47 TYR cc_start: 0.9204 (t80) cc_final: 0.8560 (t80) REVERT: J 49 SER cc_start: 0.9209 (t) cc_final: 0.8825 (p) REVERT: J 57 TYR cc_start: 0.9220 (t80) cc_final: 0.9004 (t80) REVERT: K 33 LYS cc_start: 0.9208 (mttt) cc_final: 0.8842 (mtpp) REVERT: K 37 LYS cc_start: 0.9097 (ttmt) cc_final: 0.7714 (tptt) REVERT: K 47 TYR cc_start: 0.9164 (t80) cc_final: 0.7735 (t80) REVERT: K 63 ASN cc_start: 0.8639 (m-40) cc_final: 0.8192 (m110) REVERT: L 23 LEU cc_start: 0.8684 (tp) cc_final: 0.8305 (tt) REVERT: L 26 GLN cc_start: 0.8716 (mt0) cc_final: 0.8416 (tt0) REVERT: L 37 LYS cc_start: 0.8830 (ttmt) cc_final: 0.7093 (tptt) REVERT: L 48 GLN cc_start: 0.8730 (tt0) cc_final: 0.8050 (tt0) REVERT: L 53 GLU cc_start: 0.8228 (tp30) cc_final: 0.7846 (tp30) REVERT: M 28 THR cc_start: 0.8860 (m) cc_final: 0.8156 (p) REVERT: M 31 LEU cc_start: 0.9273 (tp) cc_final: 0.8939 (tp) REVERT: M 32 ASP cc_start: 0.8367 (p0) cc_final: 0.7981 (p0) REVERT: M 39 SER cc_start: 0.9236 (m) cc_final: 0.8947 (p) REVERT: M 47 TYR cc_start: 0.9230 (t80) cc_final: 0.8556 (t80) REVERT: M 66 LYS cc_start: 0.8544 (tptt) cc_final: 0.8038 (tmtt) REVERT: N 15 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8087 (ttmm) REVERT: N 24 GLN cc_start: 0.8714 (mp10) cc_final: 0.7951 (tm-30) REVERT: N 32 ASP cc_start: 0.8194 (m-30) cc_final: 0.7932 (m-30) REVERT: N 49 SER cc_start: 0.9462 (m) cc_final: 0.9200 (t) REVERT: N 50 LYS cc_start: 0.8959 (mmtp) cc_final: 0.8473 (mmmt) REVERT: N 51 LEU cc_start: 0.9022 (tp) cc_final: 0.8748 (tt) REVERT: N 53 GLU cc_start: 0.8247 (tp30) cc_final: 0.7664 (tp30) REVERT: O 17 ASP cc_start: 0.7899 (m-30) cc_final: 0.7219 (t0) REVERT: O 22 ASN cc_start: 0.9248 (p0) cc_final: 0.8070 (p0) REVERT: O 25 THR cc_start: 0.8986 (m) cc_final: 0.8358 (p) REVERT: O 28 THR cc_start: 0.8422 (m) cc_final: 0.8120 (p) REVERT: O 33 LYS cc_start: 0.9117 (mttt) cc_final: 0.8351 (mtmm) REVERT: O 49 SER cc_start: 0.9185 (m) cc_final: 0.8957 (t) REVERT: O 50 LYS cc_start: 0.9003 (mmtt) cc_final: 0.8751 (mmpt) REVERT: O 52 SER cc_start: 0.9017 (m) cc_final: 0.8636 (t) REVERT: O 59 ASN cc_start: 0.8572 (m-40) cc_final: 0.7832 (m110) REVERT: O 69 LYS cc_start: 0.8171 (tttm) cc_final: 0.7808 (ttmt) REVERT: O 77 GLN cc_start: 0.8773 (tp-100) cc_final: 0.8519 (tp-100) REVERT: P 22 ASN cc_start: 0.9286 (p0) cc_final: 0.8891 (p0) REVERT: P 31 LEU cc_start: 0.8806 (tp) cc_final: 0.8560 (tt) REVERT: P 32 ASP cc_start: 0.8105 (m-30) cc_final: 0.7857 (m-30) REVERT: P 69 LYS cc_start: 0.8120 (tttm) cc_final: 0.7802 (ttmt) REVERT: Q 25 THR cc_start: 0.8814 (m) cc_final: 0.8226 (p) REVERT: Q 28 THR cc_start: 0.8240 (m) cc_final: 0.7992 (p) REVERT: Q 40 ASP cc_start: 0.8339 (t0) cc_final: 0.8071 (t0) REVERT: Q 54 TYR cc_start: 0.8521 (t80) cc_final: 0.7903 (t80) REVERT: Q 57 TYR cc_start: 0.8879 (t80) cc_final: 0.8403 (t80) REVERT: Q 69 LYS cc_start: 0.8369 (tttm) cc_final: 0.7735 (tttp) REVERT: R 22 ASN cc_start: 0.9067 (p0) cc_final: 0.8605 (p0) REVERT: R 24 GLN cc_start: 0.8207 (mp10) cc_final: 0.7825 (pm20) REVERT: R 29 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8013 (tm-30) REVERT: R 33 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8525 (mtmt) REVERT: S 5 TRP cc_start: 0.8369 (t60) cc_final: 0.7503 (t60) REVERT: S 17 ASP cc_start: 0.6985 (m-30) cc_final: 0.6686 (m-30) REVERT: S 29 GLU cc_start: 0.7607 (tp30) cc_final: 0.7389 (tp30) REVERT: S 39 SER cc_start: 0.9261 (m) cc_final: 0.8356 (m) REVERT: S 59 ASN cc_start: 0.8740 (m-40) cc_final: 0.7735 (m110) REVERT: S 69 LYS cc_start: 0.7855 (tttm) cc_final: 0.7527 (ttmt) REVERT: T 22 ASN cc_start: 0.8677 (p0) cc_final: 0.8336 (p0) REVERT: T 25 THR cc_start: 0.8681 (p) cc_final: 0.8205 (t) REVERT: T 39 SER cc_start: 0.9163 (m) cc_final: 0.8803 (p) REVERT: T 48 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8849 (tm-30) REVERT: T 50 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8701 (mmtt) REVERT: T 69 LYS cc_start: 0.6869 (tttm) cc_final: 0.6333 (tttt) outliers start: 51 outliers final: 40 residues processed: 586 average time/residue: 0.0971 time to fit residues: 82.3420 Evaluate side-chains 588 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 547 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.113081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096401 restraints weight = 17932.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099558 restraints weight = 9457.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101704 restraints weight = 6124.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103199 restraints weight = 4489.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104171 restraints weight = 3569.254| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11837 Z= 0.200 Angle : 0.550 9.463 16112 Z= 0.286 Chirality : 0.040 0.181 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.890 27.569 1596 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.94 % Allowed : 18.90 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1444 helix: 1.60 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.64 (0.31), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 58 TYR 0.014 0.002 TYR R 54 PHE 0.009 0.001 PHE N 68 TRP 0.010 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00457 (11837) covalent geometry : angle 0.54960 (16112) hydrogen bonds : bond 0.03627 ( 893) hydrogen bonds : angle 3.04481 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 565 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8690 (mmmt) REVERT: D 22 ASN cc_start: 0.8092 (p0) cc_final: 0.7686 (p0) REVERT: D 23 LEU cc_start: 0.7721 (tt) cc_final: 0.7454 (tt) REVERT: D 63 ASN cc_start: 0.8359 (m-40) cc_final: 0.7920 (m-40) REVERT: D 66 LYS cc_start: 0.9180 (tptp) cc_final: 0.7457 (mttt) REVERT: U 15 LYS cc_start: 0.9085 (mttt) cc_final: 0.8806 (mmtp) REVERT: U 37 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7211 (tptt) REVERT: U 66 LYS cc_start: 0.8630 (tptp) cc_final: 0.6970 (mttt) REVERT: V 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7484 (tptt) REVERT: V 47 TYR cc_start: 0.9205 (t80) cc_final: 0.8316 (t80) REVERT: V 49 SER cc_start: 0.8604 (t) cc_final: 0.8227 (p) REVERT: V 51 LEU cc_start: 0.9163 (tp) cc_final: 0.8925 (tp) REVERT: V 77 GLN cc_start: 0.8732 (tp40) cc_final: 0.7918 (tp-100) REVERT: E 37 LYS cc_start: 0.8715 (ttmt) cc_final: 0.7513 (tptt) REVERT: E 47 TYR cc_start: 0.9052 (t80) cc_final: 0.8771 (t80) REVERT: E 53 GLU cc_start: 0.8644 (tp30) cc_final: 0.8108 (mm-30) REVERT: E 66 LYS cc_start: 0.8289 (tptp) cc_final: 0.6825 (mttt) REVERT: E 69 LYS cc_start: 0.8441 (tttp) cc_final: 0.8171 (tttp) REVERT: F 28 THR cc_start: 0.8718 (m) cc_final: 0.8059 (p) REVERT: F 32 ASP cc_start: 0.7743 (m-30) cc_final: 0.7393 (m-30) REVERT: F 34 LEU cc_start: 0.9241 (tp) cc_final: 0.8958 (tt) REVERT: F 37 LYS cc_start: 0.8539 (ttmt) cc_final: 0.7891 (tptt) REVERT: F 39 SER cc_start: 0.8873 (m) cc_final: 0.8242 (t) REVERT: F 47 TYR cc_start: 0.9012 (t80) cc_final: 0.8532 (t80) REVERT: F 49 SER cc_start: 0.9283 (t) cc_final: 0.8892 (p) REVERT: F 51 LEU cc_start: 0.9203 (tp) cc_final: 0.8915 (tp) REVERT: F 53 GLU cc_start: 0.8370 (tp30) cc_final: 0.7744 (mm-30) REVERT: F 66 LYS cc_start: 0.8612 (tptp) cc_final: 0.7358 (mttm) REVERT: G 11 ASP cc_start: 0.8259 (m-30) cc_final: 0.7946 (t0) REVERT: G 15 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8805 (ttmm) REVERT: G 33 LYS cc_start: 0.9099 (mtpp) cc_final: 0.8857 (mtpp) REVERT: G 37 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7132 (tptt) REVERT: G 55 ASN cc_start: 0.8513 (t0) cc_final: 0.7762 (t0) REVERT: G 66 LYS cc_start: 0.9116 (tppt) cc_final: 0.8390 (tppt) REVERT: G 69 LYS cc_start: 0.8690 (tttm) cc_final: 0.8345 (tttt) REVERT: H 28 THR cc_start: 0.8979 (m) cc_final: 0.8359 (p) REVERT: H 32 ASP cc_start: 0.7955 (m-30) cc_final: 0.7643 (m-30) REVERT: H 37 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7012 (tptt) REVERT: H 47 TYR cc_start: 0.9099 (t80) cc_final: 0.7324 (t80) REVERT: H 51 LEU cc_start: 0.9358 (tp) cc_final: 0.8744 (tp) REVERT: H 54 TYR cc_start: 0.9024 (t80) cc_final: 0.8438 (t80) REVERT: H 77 GLN cc_start: 0.8543 (tp40) cc_final: 0.8340 (tp40) REVERT: I 28 THR cc_start: 0.9117 (m) cc_final: 0.8670 (p) REVERT: I 37 LYS cc_start: 0.8789 (ttmt) cc_final: 0.7371 (tptp) REVERT: I 47 TYR cc_start: 0.9205 (t80) cc_final: 0.8920 (t80) REVERT: I 49 SER cc_start: 0.8957 (t) cc_final: 0.8731 (t) REVERT: J 22 ASN cc_start: 0.8198 (p0) cc_final: 0.7590 (p0) REVERT: J 37 LYS cc_start: 0.8909 (ttmt) cc_final: 0.7473 (tptt) REVERT: J 47 TYR cc_start: 0.9250 (t80) cc_final: 0.8480 (t80) REVERT: J 49 SER cc_start: 0.9274 (t) cc_final: 0.8965 (p) REVERT: J 57 TYR cc_start: 0.9174 (t80) cc_final: 0.8973 (t80) REVERT: J 80 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7670 (ttp80) REVERT: K 33 LYS cc_start: 0.9210 (mttt) cc_final: 0.8806 (mtpp) REVERT: K 37 LYS cc_start: 0.9036 (ttmt) cc_final: 0.7532 (tptt) REVERT: K 47 TYR cc_start: 0.9190 (t80) cc_final: 0.7807 (t80) REVERT: K 63 ASN cc_start: 0.8681 (m-40) cc_final: 0.8410 (m110) REVERT: L 23 LEU cc_start: 0.8631 (tp) cc_final: 0.8342 (tt) REVERT: L 26 GLN cc_start: 0.8770 (mt0) cc_final: 0.8176 (tt0) REVERT: L 48 GLN cc_start: 0.8792 (tt0) cc_final: 0.8105 (tt0) REVERT: L 53 GLU cc_start: 0.8213 (tp30) cc_final: 0.7847 (tp30) REVERT: M 22 ASN cc_start: 0.8654 (p0) cc_final: 0.8345 (p0) REVERT: M 28 THR cc_start: 0.8864 (m) cc_final: 0.8155 (p) REVERT: M 31 LEU cc_start: 0.9317 (tp) cc_final: 0.8990 (tp) REVERT: M 32 ASP cc_start: 0.8408 (p0) cc_final: 0.8053 (p0) REVERT: M 47 TYR cc_start: 0.9169 (t80) cc_final: 0.8595 (t80) REVERT: M 66 LYS cc_start: 0.8592 (tptt) cc_final: 0.8098 (tmtt) REVERT: M 69 LYS cc_start: 0.8605 (tttp) cc_final: 0.7847 (ttpt) REVERT: N 24 GLN cc_start: 0.8661 (mp10) cc_final: 0.7875 (tm-30) REVERT: N 32 ASP cc_start: 0.8193 (m-30) cc_final: 0.7945 (m-30) REVERT: N 49 SER cc_start: 0.9429 (m) cc_final: 0.9193 (t) REVERT: N 50 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8503 (mmmt) REVERT: N 53 GLU cc_start: 0.8266 (tp30) cc_final: 0.7703 (tp30) REVERT: O 17 ASP cc_start: 0.8216 (m-30) cc_final: 0.7476 (t0) REVERT: O 22 ASN cc_start: 0.9253 (p0) cc_final: 0.8087 (p0) REVERT: O 25 THR cc_start: 0.8986 (m) cc_final: 0.8351 (p) REVERT: O 28 THR cc_start: 0.8448 (m) cc_final: 0.8133 (p) REVERT: O 33 LYS cc_start: 0.9112 (mttt) cc_final: 0.8350 (mtmm) REVERT: O 49 SER cc_start: 0.9208 (m) cc_final: 0.8942 (t) REVERT: O 50 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8752 (mmpt) REVERT: O 52 SER cc_start: 0.9025 (m) cc_final: 0.8800 (t) REVERT: O 59 ASN cc_start: 0.8635 (m-40) cc_final: 0.7961 (m110) REVERT: O 69 LYS cc_start: 0.8168 (tttm) cc_final: 0.7732 (ttmt) REVERT: O 77 GLN cc_start: 0.8932 (tp-100) cc_final: 0.8452 (tp-100) REVERT: P 22 ASN cc_start: 0.9256 (p0) cc_final: 0.8565 (p0) REVERT: P 31 LEU cc_start: 0.8774 (tp) cc_final: 0.8547 (tt) REVERT: P 56 LEU cc_start: 0.9148 (mp) cc_final: 0.8908 (mp) REVERT: P 69 LYS cc_start: 0.8095 (tttm) cc_final: 0.7772 (ttmt) REVERT: Q 25 THR cc_start: 0.8832 (m) cc_final: 0.8228 (p) REVERT: Q 28 THR cc_start: 0.8220 (m) cc_final: 0.8004 (p) REVERT: Q 40 ASP cc_start: 0.8256 (t0) cc_final: 0.7676 (t0) REVERT: Q 54 TYR cc_start: 0.8578 (t80) cc_final: 0.7971 (t80) REVERT: Q 57 TYR cc_start: 0.8650 (t80) cc_final: 0.8439 (t80) REVERT: Q 69 LYS cc_start: 0.8407 (tttm) cc_final: 0.7696 (tttt) REVERT: R 22 ASN cc_start: 0.9055 (p0) cc_final: 0.8618 (p0) REVERT: R 24 GLN cc_start: 0.8136 (mp10) cc_final: 0.7840 (pm20) REVERT: R 29 GLU cc_start: 0.8593 (tm-30) cc_final: 0.7984 (tm-30) REVERT: R 33 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8491 (mtmt) REVERT: R 50 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8166 (mmmt) REVERT: S 5 TRP cc_start: 0.8555 (t60) cc_final: 0.7955 (t60) REVERT: S 17 ASP cc_start: 0.7240 (m-30) cc_final: 0.6950 (m-30) REVERT: S 31 LEU cc_start: 0.9086 (tp) cc_final: 0.8742 (tt) REVERT: S 39 SER cc_start: 0.9285 (m) cc_final: 0.8337 (m) REVERT: S 59 ASN cc_start: 0.8602 (m-40) cc_final: 0.7511 (m110) REVERT: S 69 LYS cc_start: 0.7723 (tttm) cc_final: 0.7373 (ttmt) REVERT: T 22 ASN cc_start: 0.8726 (p0) cc_final: 0.8332 (p0) REVERT: T 25 THR cc_start: 0.8661 (p) cc_final: 0.8208 (t) REVERT: T 39 SER cc_start: 0.9019 (m) cc_final: 0.8815 (p) REVERT: T 48 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8878 (tm-30) REVERT: T 69 LYS cc_start: 0.6903 (tttm) cc_final: 0.6329 (tttt) outliers start: 62 outliers final: 54 residues processed: 582 average time/residue: 0.1059 time to fit residues: 88.7437 Evaluate side-chains 605 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 551 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 ASP Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 26 GLN Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 78 ASN H 63 ASN M 77 GLN N 48 GLN S 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099504 restraints weight = 17646.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102781 restraints weight = 9249.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104996 restraints weight = 5930.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106475 restraints weight = 4307.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107598 restraints weight = 3421.966| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11837 Z= 0.111 Angle : 0.483 7.134 16112 Z= 0.255 Chirality : 0.036 0.138 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.640 23.755 1596 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.39 % Allowed : 23.44 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.22), residues: 1444 helix: 1.93 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.49 (0.33), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 80 TYR 0.012 0.001 TYR G 47 PHE 0.004 0.001 PHE I 79 TRP 0.010 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00246 (11837) covalent geometry : angle 0.48315 (16112) hydrogen bonds : bond 0.03110 ( 893) hydrogen bonds : angle 2.88869 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 562 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8664 (mmmt) REVERT: D 22 ASN cc_start: 0.7990 (p0) cc_final: 0.7632 (p0) REVERT: D 23 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7393 (tt) REVERT: D 63 ASN cc_start: 0.8123 (m-40) cc_final: 0.7511 (m-40) REVERT: D 66 LYS cc_start: 0.9171 (tptp) cc_final: 0.7417 (mttt) REVERT: U 15 LYS cc_start: 0.9104 (mttt) cc_final: 0.8820 (mmtp) REVERT: U 37 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7205 (tptt) REVERT: U 66 LYS cc_start: 0.8710 (tptp) cc_final: 0.6565 (mttp) REVERT: V 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7466 (tptt) REVERT: V 47 TYR cc_start: 0.9142 (t80) cc_final: 0.8276 (t80) REVERT: V 49 SER cc_start: 0.8653 (t) cc_final: 0.8281 (p) REVERT: V 51 LEU cc_start: 0.9116 (tp) cc_final: 0.8879 (tt) REVERT: V 77 GLN cc_start: 0.8710 (tp40) cc_final: 0.8152 (tp40) REVERT: E 22 ASN cc_start: 0.7635 (p0) cc_final: 0.6965 (p0) REVERT: E 37 LYS cc_start: 0.8751 (ttmt) cc_final: 0.7532 (tptt) REVERT: E 53 GLU cc_start: 0.8515 (tp30) cc_final: 0.8008 (mm-30) REVERT: E 66 LYS cc_start: 0.8330 (tptp) cc_final: 0.6846 (mttt) REVERT: F 28 THR cc_start: 0.8692 (m) cc_final: 0.8079 (p) REVERT: F 32 ASP cc_start: 0.7708 (m-30) cc_final: 0.7355 (m-30) REVERT: F 34 LEU cc_start: 0.9207 (tp) cc_final: 0.8934 (tt) REVERT: F 37 LYS cc_start: 0.8595 (ttmt) cc_final: 0.7743 (tptt) REVERT: F 39 SER cc_start: 0.8846 (m) cc_final: 0.8200 (t) REVERT: F 47 TYR cc_start: 0.8878 (t80) cc_final: 0.8212 (t80) REVERT: F 49 SER cc_start: 0.9239 (t) cc_final: 0.8792 (p) REVERT: F 53 GLU cc_start: 0.8102 (tp30) cc_final: 0.7520 (mm-30) REVERT: F 63 ASN cc_start: 0.9142 (m-40) cc_final: 0.8901 (m110) REVERT: F 66 LYS cc_start: 0.8496 (tptp) cc_final: 0.7590 (ttmt) REVERT: G 11 ASP cc_start: 0.8114 (m-30) cc_final: 0.7874 (t0) REVERT: G 15 LYS cc_start: 0.9102 (ttmt) cc_final: 0.8720 (ttmm) REVERT: G 33 LYS cc_start: 0.9277 (mtpp) cc_final: 0.9019 (mtpp) REVERT: G 37 LYS cc_start: 0.8336 (ttmt) cc_final: 0.7129 (tptt) REVERT: G 66 LYS cc_start: 0.8952 (tppt) cc_final: 0.8407 (tppt) REVERT: G 69 LYS cc_start: 0.8714 (tttm) cc_final: 0.8420 (tttt) REVERT: H 28 THR cc_start: 0.8935 (m) cc_final: 0.8393 (p) REVERT: H 32 ASP cc_start: 0.7817 (m-30) cc_final: 0.7495 (m-30) REVERT: H 37 LYS cc_start: 0.8300 (ttmt) cc_final: 0.6949 (tptt) REVERT: H 47 TYR cc_start: 0.9042 (t80) cc_final: 0.7328 (t80) REVERT: H 51 LEU cc_start: 0.9338 (tp) cc_final: 0.8766 (tp) REVERT: H 77 GLN cc_start: 0.8569 (tp40) cc_final: 0.8364 (tp40) REVERT: I 28 THR cc_start: 0.9000 (m) cc_final: 0.8788 (p) REVERT: I 37 LYS cc_start: 0.8708 (ttmt) cc_final: 0.7230 (tptp) REVERT: I 47 TYR cc_start: 0.9158 (t80) cc_final: 0.8787 (t80) REVERT: I 49 SER cc_start: 0.8955 (t) cc_final: 0.8732 (t) REVERT: I 76 ILE cc_start: 0.9714 (mm) cc_final: 0.9378 (tt) REVERT: I 78 ASN cc_start: 0.9285 (m-40) cc_final: 0.8906 (m-40) REVERT: J 22 ASN cc_start: 0.8197 (p0) cc_final: 0.7610 (p0) REVERT: J 37 LYS cc_start: 0.8829 (ttmt) cc_final: 0.7412 (tptt) REVERT: J 49 SER cc_start: 0.9268 (t) cc_final: 0.8943 (p) REVERT: K 33 LYS cc_start: 0.9266 (mttt) cc_final: 0.8867 (mtpp) REVERT: K 37 LYS cc_start: 0.8987 (ttmt) cc_final: 0.7561 (tptp) REVERT: K 47 TYR cc_start: 0.9146 (t80) cc_final: 0.7780 (t80) REVERT: K 63 ASN cc_start: 0.8542 (m-40) cc_final: 0.8203 (m110) REVERT: L 23 LEU cc_start: 0.8676 (tp) cc_final: 0.8200 (tt) REVERT: L 26 GLN cc_start: 0.8751 (mt0) cc_final: 0.8267 (tt0) REVERT: L 53 GLU cc_start: 0.8155 (tp30) cc_final: 0.7846 (tp30) REVERT: L 77 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8073 (tp40) REVERT: M 22 ASN cc_start: 0.8597 (p0) cc_final: 0.8161 (p0) REVERT: M 28 THR cc_start: 0.8836 (m) cc_final: 0.8102 (p) REVERT: M 31 LEU cc_start: 0.9320 (tp) cc_final: 0.9013 (tp) REVERT: M 32 ASP cc_start: 0.8385 (p0) cc_final: 0.8041 (p0) REVERT: M 47 TYR cc_start: 0.9278 (t80) cc_final: 0.8673 (t80) REVERT: M 66 LYS cc_start: 0.8684 (tptt) cc_final: 0.8150 (tmtt) REVERT: M 69 LYS cc_start: 0.8579 (tttp) cc_final: 0.7834 (ttpt) REVERT: N 24 GLN cc_start: 0.8601 (mp10) cc_final: 0.7904 (tm-30) REVERT: N 32 ASP cc_start: 0.8233 (m-30) cc_final: 0.7977 (m-30) REVERT: N 47 TYR cc_start: 0.8934 (t80) cc_final: 0.8615 (t80) REVERT: N 49 SER cc_start: 0.9417 (m) cc_final: 0.9143 (t) REVERT: N 53 GLU cc_start: 0.8193 (tp30) cc_final: 0.7569 (tp30) REVERT: O 15 LYS cc_start: 0.8753 (tppt) cc_final: 0.8543 (tptp) REVERT: O 17 ASP cc_start: 0.8180 (m-30) cc_final: 0.7441 (t0) REVERT: O 22 ASN cc_start: 0.9208 (p0) cc_final: 0.8056 (p0) REVERT: O 25 THR cc_start: 0.8938 (m) cc_final: 0.8370 (p) REVERT: O 28 THR cc_start: 0.8474 (m) cc_final: 0.8139 (p) REVERT: O 33 LYS cc_start: 0.9086 (mttt) cc_final: 0.8321 (mtmm) REVERT: O 49 SER cc_start: 0.9197 (m) cc_final: 0.8913 (t) REVERT: O 50 LYS cc_start: 0.9007 (mmtt) cc_final: 0.8804 (mmpt) REVERT: O 59 ASN cc_start: 0.8518 (m-40) cc_final: 0.7821 (m110) REVERT: O 69 LYS cc_start: 0.8176 (tttm) cc_final: 0.7682 (ttmt) REVERT: O 77 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8291 (tp-100) REVERT: P 22 ASN cc_start: 0.9254 (p0) cc_final: 0.8651 (p0) REVERT: P 23 LEU cc_start: 0.8816 (tp) cc_final: 0.8432 (tt) REVERT: P 29 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: Q 25 THR cc_start: 0.8783 (m) cc_final: 0.8215 (p) REVERT: Q 31 LEU cc_start: 0.8788 (tp) cc_final: 0.8572 (tp) REVERT: Q 40 ASP cc_start: 0.8118 (t0) cc_final: 0.7863 (t0) REVERT: Q 54 TYR cc_start: 0.8500 (t80) cc_final: 0.7873 (t80) REVERT: Q 57 TYR cc_start: 0.8659 (t80) cc_final: 0.8388 (t80) REVERT: Q 69 LYS cc_start: 0.8348 (tttm) cc_final: 0.7681 (tttp) REVERT: R 17 ASP cc_start: 0.7380 (m-30) cc_final: 0.7155 (m-30) REVERT: R 22 ASN cc_start: 0.9067 (p0) cc_final: 0.8675 (p0) REVERT: R 24 GLN cc_start: 0.8176 (mp10) cc_final: 0.7596 (pm20) REVERT: R 29 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8114 (tm-30) REVERT: R 69 LYS cc_start: 0.8172 (tttm) cc_final: 0.7125 (mttt) REVERT: S 17 ASP cc_start: 0.7619 (m-30) cc_final: 0.7220 (m-30) REVERT: S 39 SER cc_start: 0.9288 (m) cc_final: 0.8362 (m) REVERT: S 59 ASN cc_start: 0.8684 (m-40) cc_final: 0.7580 (m110) REVERT: T 22 ASN cc_start: 0.8656 (p0) cc_final: 0.8274 (p0) REVERT: T 25 THR cc_start: 0.8557 (p) cc_final: 0.8073 (t) REVERT: T 39 SER cc_start: 0.9124 (m) cc_final: 0.8779 (p) REVERT: T 48 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8520 (tm-30) REVERT: T 50 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8609 (mmmt) REVERT: T 69 LYS cc_start: 0.6914 (tttm) cc_final: 0.6327 (tttt) outliers start: 30 outliers final: 20 residues processed: 568 average time/residue: 0.1046 time to fit residues: 85.3141 Evaluate side-chains 567 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 545 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 6 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain T residue 13 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 0.0980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN G 55 ASN K 55 ASN L 48 GLN M 77 GLN S 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098721 restraints weight = 17698.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101890 restraints weight = 9366.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104128 restraints weight = 6066.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105634 restraints weight = 4417.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106710 restraints weight = 3496.585| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11837 Z= 0.126 Angle : 0.503 8.593 16112 Z= 0.261 Chirality : 0.038 0.176 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.592 23.998 1596 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.87 % Allowed : 24.16 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.22), residues: 1444 helix: 2.05 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.32 (0.36), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG V 58 TYR 0.011 0.001 TYR J 47 PHE 0.005 0.001 PHE J 16 TRP 0.010 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00288 (11837) covalent geometry : angle 0.50339 (16112) hydrogen bonds : bond 0.03135 ( 893) hydrogen bonds : angle 2.89180 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 550 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8657 (mmmt) REVERT: D 22 ASN cc_start: 0.8012 (p0) cc_final: 0.7630 (p0) REVERT: D 23 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7507 (tt) REVERT: D 66 LYS cc_start: 0.9012 (tptp) cc_final: 0.7460 (mttt) REVERT: U 15 LYS cc_start: 0.9037 (mttt) cc_final: 0.8774 (mmtp) REVERT: U 37 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7211 (tptt) REVERT: U 66 LYS cc_start: 0.8696 (tptp) cc_final: 0.6570 (mttp) REVERT: U 77 GLN cc_start: 0.8892 (tp40) cc_final: 0.8662 (tp40) REVERT: V 37 LYS cc_start: 0.8698 (ttmt) cc_final: 0.7457 (tptt) REVERT: V 47 TYR cc_start: 0.9170 (t80) cc_final: 0.8337 (t80) REVERT: V 49 SER cc_start: 0.8656 (t) cc_final: 0.8279 (p) REVERT: V 51 LEU cc_start: 0.9107 (tp) cc_final: 0.8873 (tp) REVERT: V 77 GLN cc_start: 0.8745 (tp40) cc_final: 0.8183 (tp40) REVERT: E 22 ASN cc_start: 0.7709 (p0) cc_final: 0.7018 (p0) REVERT: E 37 LYS cc_start: 0.8722 (ttmt) cc_final: 0.7465 (tptt) REVERT: E 53 GLU cc_start: 0.8598 (tp30) cc_final: 0.8117 (mm-30) REVERT: E 66 LYS cc_start: 0.8407 (tptp) cc_final: 0.6877 (mttt) REVERT: F 28 THR cc_start: 0.8709 (m) cc_final: 0.8090 (p) REVERT: F 32 ASP cc_start: 0.7711 (m-30) cc_final: 0.7366 (m-30) REVERT: F 34 LEU cc_start: 0.9201 (tp) cc_final: 0.8935 (tt) REVERT: F 37 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7844 (tptt) REVERT: F 39 SER cc_start: 0.8825 (m) cc_final: 0.8201 (t) REVERT: F 47 TYR cc_start: 0.8915 (t80) cc_final: 0.8312 (t80) REVERT: F 49 SER cc_start: 0.9250 (t) cc_final: 0.8804 (p) REVERT: F 53 GLU cc_start: 0.8130 (tp30) cc_final: 0.7564 (mm-30) REVERT: F 63 ASN cc_start: 0.9038 (m-40) cc_final: 0.8819 (m110) REVERT: F 66 LYS cc_start: 0.8468 (tptp) cc_final: 0.7568 (ttmt) REVERT: G 11 ASP cc_start: 0.8127 (m-30) cc_final: 0.7875 (t0) REVERT: G 15 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8707 (ttmm) REVERT: G 33 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9022 (mtpp) REVERT: G 37 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7103 (tptt) REVERT: G 66 LYS cc_start: 0.8989 (tppt) cc_final: 0.8420 (tppt) REVERT: G 69 LYS cc_start: 0.8708 (tttm) cc_final: 0.8415 (tttt) REVERT: H 28 THR cc_start: 0.8955 (m) cc_final: 0.8388 (p) REVERT: H 32 ASP cc_start: 0.7745 (m-30) cc_final: 0.7403 (m-30) REVERT: H 37 LYS cc_start: 0.8275 (ttmt) cc_final: 0.6940 (tptt) REVERT: H 47 TYR cc_start: 0.9063 (t80) cc_final: 0.7343 (t80) REVERT: H 51 LEU cc_start: 0.9337 (tp) cc_final: 0.8776 (tp) REVERT: I 37 LYS cc_start: 0.8668 (ttmt) cc_final: 0.7199 (tptp) REVERT: I 47 TYR cc_start: 0.9163 (t80) cc_final: 0.8851 (t80) REVERT: I 49 SER cc_start: 0.8950 (t) cc_final: 0.8727 (t) REVERT: I 78 ASN cc_start: 0.9292 (m-40) cc_final: 0.8922 (m-40) REVERT: J 22 ASN cc_start: 0.8173 (p0) cc_final: 0.7657 (p0) REVERT: J 31 LEU cc_start: 0.8276 (tp) cc_final: 0.7683 (mt) REVERT: J 37 LYS cc_start: 0.8748 (ttmt) cc_final: 0.7501 (tptt) REVERT: J 47 TYR cc_start: 0.9185 (t80) cc_final: 0.8336 (t80) REVERT: J 49 SER cc_start: 0.9242 (t) cc_final: 0.8964 (p) REVERT: J 51 LEU cc_start: 0.9233 (tp) cc_final: 0.8881 (tp) REVERT: K 15 LYS cc_start: 0.9176 (tptm) cc_final: 0.8891 (tptm) REVERT: K 33 LYS cc_start: 0.9275 (mttt) cc_final: 0.8862 (mtpp) REVERT: K 37 LYS cc_start: 0.8968 (ttmt) cc_final: 0.7533 (tptp) REVERT: K 47 TYR cc_start: 0.9151 (t80) cc_final: 0.7797 (t80) REVERT: L 23 LEU cc_start: 0.8780 (tp) cc_final: 0.8392 (tt) REVERT: L 26 GLN cc_start: 0.8732 (mt0) cc_final: 0.8312 (tt0) REVERT: L 53 GLU cc_start: 0.8206 (tp30) cc_final: 0.7853 (tp30) REVERT: L 77 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8092 (tp40) REVERT: M 22 ASN cc_start: 0.8573 (p0) cc_final: 0.8154 (p0) REVERT: M 28 THR cc_start: 0.8817 (m) cc_final: 0.8075 (p) REVERT: M 31 LEU cc_start: 0.9318 (tp) cc_final: 0.9010 (tp) REVERT: M 32 ASP cc_start: 0.8371 (p0) cc_final: 0.8033 (p0) REVERT: M 47 TYR cc_start: 0.9290 (t80) cc_final: 0.8657 (t80) REVERT: M 66 LYS cc_start: 0.8706 (tptt) cc_final: 0.8192 (tmtt) REVERT: M 69 LYS cc_start: 0.8568 (tttp) cc_final: 0.7856 (ttpt) REVERT: N 24 GLN cc_start: 0.8567 (mp10) cc_final: 0.7901 (tm-30) REVERT: N 32 ASP cc_start: 0.8232 (m-30) cc_final: 0.7951 (m-30) REVERT: N 49 SER cc_start: 0.9419 (m) cc_final: 0.9134 (t) REVERT: N 53 GLU cc_start: 0.8174 (tp30) cc_final: 0.7560 (tp30) REVERT: O 15 LYS cc_start: 0.8697 (tppt) cc_final: 0.8457 (tptp) REVERT: O 17 ASP cc_start: 0.8256 (m-30) cc_final: 0.7434 (t0) REVERT: O 22 ASN cc_start: 0.9180 (p0) cc_final: 0.7977 (p0) REVERT: O 25 THR cc_start: 0.9025 (m) cc_final: 0.8425 (p) REVERT: O 28 THR cc_start: 0.8461 (m) cc_final: 0.8108 (p) REVERT: O 33 LYS cc_start: 0.9081 (mttt) cc_final: 0.8310 (mtmm) REVERT: O 49 SER cc_start: 0.9154 (m) cc_final: 0.8883 (t) REVERT: O 50 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8802 (mmpt) REVERT: O 59 ASN cc_start: 0.8544 (m-40) cc_final: 0.7960 (m110) REVERT: O 69 LYS cc_start: 0.8075 (tttm) cc_final: 0.7557 (ttmt) REVERT: O 77 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8431 (tp-100) REVERT: P 22 ASN cc_start: 0.9254 (p0) cc_final: 0.8644 (p0) REVERT: P 23 LEU cc_start: 0.8847 (tp) cc_final: 0.8407 (tt) REVERT: P 29 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: P 33 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8910 (ttmt) REVERT: Q 25 THR cc_start: 0.8641 (m) cc_final: 0.8350 (p) REVERT: Q 31 LEU cc_start: 0.8765 (tp) cc_final: 0.8549 (tp) REVERT: Q 40 ASP cc_start: 0.8119 (t0) cc_final: 0.7858 (t0) REVERT: Q 54 TYR cc_start: 0.8516 (t80) cc_final: 0.7859 (t80) REVERT: Q 69 LYS cc_start: 0.8363 (tttm) cc_final: 0.7908 (ttmt) REVERT: R 17 ASP cc_start: 0.7425 (m-30) cc_final: 0.7202 (m-30) REVERT: R 24 GLN cc_start: 0.8179 (mp10) cc_final: 0.7562 (pm20) REVERT: R 69 LYS cc_start: 0.8194 (tttm) cc_final: 0.6929 (mttt) REVERT: S 17 ASP cc_start: 0.7717 (m-30) cc_final: 0.7314 (m-30) REVERT: S 39 SER cc_start: 0.9298 (m) cc_final: 0.8372 (m) REVERT: S 59 ASN cc_start: 0.8699 (m-40) cc_final: 0.7553 (m110) REVERT: T 17 ASP cc_start: 0.8537 (m-30) cc_final: 0.8298 (m-30) REVERT: T 22 ASN cc_start: 0.8658 (p0) cc_final: 0.8244 (p0) REVERT: T 25 THR cc_start: 0.8573 (p) cc_final: 0.8096 (t) REVERT: T 39 SER cc_start: 0.9040 (m) cc_final: 0.8703 (p) REVERT: T 48 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8515 (tm-30) REVERT: T 50 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8605 (mmmt) REVERT: T 69 LYS cc_start: 0.6886 (tttm) cc_final: 0.6276 (tttt) outliers start: 36 outliers final: 31 residues processed: 561 average time/residue: 0.1018 time to fit residues: 82.3733 Evaluate side-chains 574 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 541 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 73 optimal weight: 0.0370 chunk 117 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN M 77 GLN O 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095863 restraints weight = 17772.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099035 restraints weight = 9323.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101261 restraints weight = 5998.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102776 restraints weight = 4366.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103781 restraints weight = 3455.264| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11837 Z= 0.171 Angle : 0.544 8.122 16112 Z= 0.282 Chirality : 0.039 0.169 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.677 25.999 1596 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.11 % Allowed : 24.80 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.22), residues: 1444 helix: 2.06 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.23 (0.37), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 58 TYR 0.031 0.002 TYR E 47 PHE 0.010 0.001 PHE M 79 TRP 0.010 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00395 (11837) covalent geometry : angle 0.54361 (16112) hydrogen bonds : bond 0.03260 ( 893) hydrogen bonds : angle 2.93508 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 555 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8686 (mmmt) REVERT: D 22 ASN cc_start: 0.8100 (p0) cc_final: 0.7798 (p0) REVERT: D 37 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7518 (tptt) REVERT: D 56 LEU cc_start: 0.8939 (mt) cc_final: 0.8720 (mt) REVERT: U 15 LYS cc_start: 0.9050 (mttt) cc_final: 0.8795 (mmtp) REVERT: U 37 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7221 (tptt) REVERT: U 66 LYS cc_start: 0.8688 (tptp) cc_final: 0.6564 (mttp) REVERT: U 77 GLN cc_start: 0.8922 (tp40) cc_final: 0.8692 (tp40) REVERT: V 15 LYS cc_start: 0.9231 (tppp) cc_final: 0.9019 (mmtp) REVERT: V 37 LYS cc_start: 0.8773 (ttmt) cc_final: 0.7564 (tptt) REVERT: V 49 SER cc_start: 0.8656 (t) cc_final: 0.8257 (p) REVERT: V 51 LEU cc_start: 0.9123 (tp) cc_final: 0.8911 (tp) REVERT: V 77 GLN cc_start: 0.8758 (tp40) cc_final: 0.8213 (tp40) REVERT: E 22 ASN cc_start: 0.8185 (p0) cc_final: 0.7529 (p0) REVERT: E 37 LYS cc_start: 0.8748 (ttmt) cc_final: 0.7438 (tptt) REVERT: E 53 GLU cc_start: 0.8601 (tp30) cc_final: 0.8110 (mm-30) REVERT: E 66 LYS cc_start: 0.8371 (tptp) cc_final: 0.6889 (mttt) REVERT: F 34 LEU cc_start: 0.9227 (tp) cc_final: 0.8957 (tt) REVERT: F 37 LYS cc_start: 0.8629 (ttmt) cc_final: 0.7850 (tptt) REVERT: F 39 SER cc_start: 0.8867 (m) cc_final: 0.8202 (t) REVERT: F 47 TYR cc_start: 0.9023 (t80) cc_final: 0.8353 (t80) REVERT: F 49 SER cc_start: 0.9272 (t) cc_final: 0.8852 (p) REVERT: F 53 GLU cc_start: 0.8394 (tp30) cc_final: 0.7881 (mm-30) REVERT: F 63 ASN cc_start: 0.9078 (m-40) cc_final: 0.8851 (m110) REVERT: F 66 LYS cc_start: 0.8442 (tptp) cc_final: 0.7551 (ttmt) REVERT: G 11 ASP cc_start: 0.8249 (m-30) cc_final: 0.7925 (t0) REVERT: G 15 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8770 (ttmm) REVERT: G 33 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8893 (mtpp) REVERT: G 37 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7059 (tptt) REVERT: G 66 LYS cc_start: 0.8963 (tppt) cc_final: 0.8427 (tppt) REVERT: G 69 LYS cc_start: 0.8705 (tttm) cc_final: 0.8353 (tttt) REVERT: H 28 THR cc_start: 0.8963 (m) cc_final: 0.8424 (p) REVERT: H 32 ASP cc_start: 0.7943 (m-30) cc_final: 0.7642 (m-30) REVERT: H 37 LYS cc_start: 0.8340 (ttmt) cc_final: 0.6971 (tptt) REVERT: H 47 TYR cc_start: 0.9083 (t80) cc_final: 0.7309 (t80) REVERT: H 51 LEU cc_start: 0.9342 (tp) cc_final: 0.8720 (tp) REVERT: H 54 TYR cc_start: 0.8970 (t80) cc_final: 0.8353 (t80) REVERT: I 37 LYS cc_start: 0.8720 (ttmt) cc_final: 0.7288 (tptp) REVERT: I 49 SER cc_start: 0.8927 (t) cc_final: 0.8704 (t) REVERT: I 76 ILE cc_start: 0.9732 (mm) cc_final: 0.9399 (tt) REVERT: I 78 ASN cc_start: 0.9431 (m-40) cc_final: 0.9123 (m-40) REVERT: J 22 ASN cc_start: 0.8313 (p0) cc_final: 0.7787 (p0) REVERT: J 31 LEU cc_start: 0.8299 (tp) cc_final: 0.8022 (mt) REVERT: J 37 LYS cc_start: 0.8814 (ttmt) cc_final: 0.7385 (tptt) REVERT: J 47 TYR cc_start: 0.9193 (t80) cc_final: 0.8415 (t80) REVERT: J 49 SER cc_start: 0.9260 (t) cc_final: 0.8960 (p) REVERT: K 15 LYS cc_start: 0.9162 (tptm) cc_final: 0.8872 (tptm) REVERT: K 33 LYS cc_start: 0.9270 (mttt) cc_final: 0.8862 (mtpp) REVERT: K 37 LYS cc_start: 0.8979 (ttmt) cc_final: 0.7517 (tptp) REVERT: K 47 TYR cc_start: 0.9156 (t80) cc_final: 0.7795 (t80) REVERT: L 26 GLN cc_start: 0.8944 (mt0) cc_final: 0.8402 (mt0) REVERT: L 53 GLU cc_start: 0.8193 (tp30) cc_final: 0.7856 (tp30) REVERT: L 77 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8168 (tp40) REVERT: M 22 ASN cc_start: 0.8639 (p0) cc_final: 0.8235 (p0) REVERT: M 28 THR cc_start: 0.8792 (m) cc_final: 0.8033 (p) REVERT: M 31 LEU cc_start: 0.9305 (tp) cc_final: 0.8970 (tp) REVERT: M 32 ASP cc_start: 0.8369 (p0) cc_final: 0.8023 (p0) REVERT: M 47 TYR cc_start: 0.9179 (t80) cc_final: 0.8480 (t80) REVERT: M 66 LYS cc_start: 0.8524 (tptt) cc_final: 0.7987 (tmtt) REVERT: M 69 LYS cc_start: 0.8598 (tttp) cc_final: 0.7870 (ttpt) REVERT: N 24 GLN cc_start: 0.8561 (mp10) cc_final: 0.7839 (tm-30) REVERT: N 32 ASP cc_start: 0.8247 (m-30) cc_final: 0.7969 (m-30) REVERT: N 49 SER cc_start: 0.9424 (m) cc_final: 0.9169 (t) REVERT: N 50 LYS cc_start: 0.8921 (mmtp) cc_final: 0.8445 (mmmt) REVERT: N 53 GLU cc_start: 0.8231 (tp30) cc_final: 0.7633 (tp30) REVERT: O 15 LYS cc_start: 0.8676 (tppt) cc_final: 0.8411 (tptp) REVERT: O 17 ASP cc_start: 0.8292 (m-30) cc_final: 0.7373 (t0) REVERT: O 22 ASN cc_start: 0.9220 (p0) cc_final: 0.7999 (p0) REVERT: O 25 THR cc_start: 0.9032 (m) cc_final: 0.8444 (p) REVERT: O 28 THR cc_start: 0.8417 (m) cc_final: 0.8112 (p) REVERT: O 33 LYS cc_start: 0.9098 (mttt) cc_final: 0.8325 (mtmm) REVERT: O 49 SER cc_start: 0.9211 (m) cc_final: 0.8668 (t) REVERT: O 50 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8738 (mmpt) REVERT: O 59 ASN cc_start: 0.8585 (m-40) cc_final: 0.7902 (m110) REVERT: O 69 LYS cc_start: 0.8095 (tttm) cc_final: 0.7547 (ttmt) REVERT: O 77 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8547 (tp-100) REVERT: P 22 ASN cc_start: 0.9292 (p0) cc_final: 0.8751 (p0) REVERT: P 23 LEU cc_start: 0.8831 (tp) cc_final: 0.8405 (tt) REVERT: P 29 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: Q 25 THR cc_start: 0.8668 (m) cc_final: 0.8381 (p) REVERT: Q 40 ASP cc_start: 0.8207 (t0) cc_final: 0.7688 (t70) REVERT: Q 54 TYR cc_start: 0.8511 (t80) cc_final: 0.7977 (t80) REVERT: Q 69 LYS cc_start: 0.8383 (tttm) cc_final: 0.7925 (ttmt) REVERT: R 17 ASP cc_start: 0.7519 (m-30) cc_final: 0.7277 (m-30) REVERT: R 24 GLN cc_start: 0.8192 (mp10) cc_final: 0.7561 (pm20) REVERT: R 50 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8172 (mmmt) REVERT: R 69 LYS cc_start: 0.8215 (tttm) cc_final: 0.6913 (mttt) REVERT: S 17 ASP cc_start: 0.7743 (m-30) cc_final: 0.7307 (m-30) REVERT: S 33 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8272 (mttp) REVERT: S 39 SER cc_start: 0.9332 (m) cc_final: 0.8412 (m) REVERT: S 58 ARG cc_start: 0.9023 (mmt180) cc_final: 0.8744 (mmt90) REVERT: S 59 ASN cc_start: 0.8748 (m-40) cc_final: 0.7574 (m110) REVERT: T 17 ASP cc_start: 0.8062 (m-30) cc_final: 0.7833 (m-30) REVERT: T 22 ASN cc_start: 0.8860 (p0) cc_final: 0.8473 (p0) REVERT: T 25 THR cc_start: 0.8620 (p) cc_final: 0.8142 (t) REVERT: T 39 SER cc_start: 0.9060 (m) cc_final: 0.8751 (p) REVERT: T 48 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8536 (tm-30) REVERT: T 50 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8522 (mmmt) REVERT: T 69 LYS cc_start: 0.6904 (tttm) cc_final: 0.6309 (tttt) outliers start: 39 outliers final: 33 residues processed: 568 average time/residue: 0.1076 time to fit residues: 87.6483 Evaluate side-chains 584 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 550 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN M 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098284 restraints weight = 17515.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.101463 restraints weight = 9226.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103687 restraints weight = 5960.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105205 restraints weight = 4324.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106255 restraints weight = 3424.303| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11837 Z= 0.124 Angle : 0.524 7.676 16112 Z= 0.270 Chirality : 0.037 0.149 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.548 23.617 1596 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.47 % Allowed : 26.40 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.22), residues: 1444 helix: 2.19 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.11 (0.38), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 80 TYR 0.025 0.001 TYR E 47 PHE 0.005 0.001 PHE J 16 TRP 0.011 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00286 (11837) covalent geometry : angle 0.52370 (16112) hydrogen bonds : bond 0.03034 ( 893) hydrogen bonds : angle 2.86135 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 558 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8885 (mmmm) cc_final: 0.8668 (mmmt) REVERT: D 37 LYS cc_start: 0.8589 (ttmt) cc_final: 0.7562 (tptt) REVERT: D 77 GLN cc_start: 0.8578 (tp40) cc_final: 0.8330 (tp-100) REVERT: U 15 LYS cc_start: 0.9032 (mttt) cc_final: 0.8791 (mmtp) REVERT: U 37 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7243 (tptt) REVERT: U 66 LYS cc_start: 0.8693 (tptp) cc_final: 0.6571 (mttp) REVERT: U 77 GLN cc_start: 0.8847 (tp40) cc_final: 0.8630 (tp40) REVERT: V 15 LYS cc_start: 0.9224 (tppp) cc_final: 0.9008 (mmtp) REVERT: V 37 LYS cc_start: 0.8699 (ttmt) cc_final: 0.7449 (tptt) REVERT: V 47 TYR cc_start: 0.9151 (t80) cc_final: 0.8169 (t80) REVERT: V 49 SER cc_start: 0.8635 (t) cc_final: 0.8250 (p) REVERT: V 51 LEU cc_start: 0.9114 (tp) cc_final: 0.8888 (tp) REVERT: V 77 GLN cc_start: 0.8731 (tp40) cc_final: 0.8152 (tp40) REVERT: E 22 ASN cc_start: 0.8003 (p0) cc_final: 0.7339 (p0) REVERT: E 37 LYS cc_start: 0.8760 (ttmt) cc_final: 0.7458 (tptt) REVERT: E 66 LYS cc_start: 0.8344 (tptp) cc_final: 0.6769 (mttt) REVERT: F 34 LEU cc_start: 0.9218 (tp) cc_final: 0.8950 (tt) REVERT: F 37 LYS cc_start: 0.8646 (ttmt) cc_final: 0.7747 (tptt) REVERT: F 39 SER cc_start: 0.8811 (m) cc_final: 0.8194 (t) REVERT: F 47 TYR cc_start: 0.8946 (t80) cc_final: 0.8291 (t80) REVERT: F 49 SER cc_start: 0.9241 (t) cc_final: 0.8785 (p) REVERT: F 53 GLU cc_start: 0.8196 (tp30) cc_final: 0.7728 (mm-30) REVERT: F 66 LYS cc_start: 0.8426 (tptp) cc_final: 0.7568 (ttmt) REVERT: G 11 ASP cc_start: 0.8123 (m-30) cc_final: 0.7859 (t0) REVERT: G 15 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8682 (ttmm) REVERT: G 33 LYS cc_start: 0.9297 (mtpp) cc_final: 0.9058 (mtpp) REVERT: G 37 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7057 (tptt) REVERT: G 66 LYS cc_start: 0.8964 (tppt) cc_final: 0.8564 (tppt) REVERT: G 69 LYS cc_start: 0.8724 (tttm) cc_final: 0.8491 (tttt) REVERT: H 28 THR cc_start: 0.8967 (m) cc_final: 0.8413 (p) REVERT: H 32 ASP cc_start: 0.7828 (m-30) cc_final: 0.7513 (m-30) REVERT: H 37 LYS cc_start: 0.8248 (ttmt) cc_final: 0.6924 (tptt) REVERT: H 47 TYR cc_start: 0.9036 (t80) cc_final: 0.7291 (t80) REVERT: H 51 LEU cc_start: 0.9331 (tp) cc_final: 0.8755 (tp) REVERT: I 37 LYS cc_start: 0.8535 (ttmt) cc_final: 0.6960 (tptp) REVERT: I 49 SER cc_start: 0.8938 (t) cc_final: 0.8683 (t) REVERT: I 76 ILE cc_start: 0.9732 (mm) cc_final: 0.9396 (tt) REVERT: I 78 ASN cc_start: 0.9292 (m-40) cc_final: 0.8977 (m-40) REVERT: J 22 ASN cc_start: 0.8268 (p0) cc_final: 0.7737 (p0) REVERT: J 37 LYS cc_start: 0.8747 (ttmt) cc_final: 0.7498 (tptt) REVERT: J 47 TYR cc_start: 0.9150 (t80) cc_final: 0.8398 (t80) REVERT: J 49 SER cc_start: 0.9248 (t) cc_final: 0.8966 (p) REVERT: K 33 LYS cc_start: 0.9272 (mttt) cc_final: 0.8853 (mtpp) REVERT: K 37 LYS cc_start: 0.8946 (ttmt) cc_final: 0.7501 (tptp) REVERT: K 47 TYR cc_start: 0.9036 (t80) cc_final: 0.7759 (t80) REVERT: K 63 ASN cc_start: 0.8634 (m-40) cc_final: 0.8327 (m110) REVERT: L 26 GLN cc_start: 0.8886 (mt0) cc_final: 0.8263 (tt0) REVERT: L 53 GLU cc_start: 0.8167 (tp30) cc_final: 0.7854 (tp30) REVERT: L 77 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8370 (tp40) REVERT: M 22 ASN cc_start: 0.8554 (p0) cc_final: 0.8205 (p0) REVERT: M 28 THR cc_start: 0.8765 (m) cc_final: 0.7988 (p) REVERT: M 31 LEU cc_start: 0.9316 (tp) cc_final: 0.9000 (tp) REVERT: M 32 ASP cc_start: 0.8372 (p0) cc_final: 0.8010 (p0) REVERT: M 47 TYR cc_start: 0.9131 (t80) cc_final: 0.8497 (t80) REVERT: M 66 LYS cc_start: 0.8682 (tptt) cc_final: 0.8169 (tmtt) REVERT: M 69 LYS cc_start: 0.8551 (tttp) cc_final: 0.7823 (ttpt) REVERT: N 8 TYR cc_start: 0.8770 (t80) cc_final: 0.8556 (t80) REVERT: N 24 GLN cc_start: 0.8537 (mp10) cc_final: 0.7845 (tm-30) REVERT: N 32 ASP cc_start: 0.8256 (m-30) cc_final: 0.7995 (m-30) REVERT: N 49 SER cc_start: 0.9366 (m) cc_final: 0.9158 (t) REVERT: N 53 GLU cc_start: 0.8278 (tp30) cc_final: 0.7716 (tp30) REVERT: O 15 LYS cc_start: 0.8663 (tppt) cc_final: 0.8408 (tptp) REVERT: O 17 ASP cc_start: 0.8266 (m-30) cc_final: 0.7365 (t0) REVERT: O 22 ASN cc_start: 0.9167 (p0) cc_final: 0.7923 (p0) REVERT: O 25 THR cc_start: 0.9022 (m) cc_final: 0.8445 (p) REVERT: O 28 THR cc_start: 0.8468 (m) cc_final: 0.8127 (p) REVERT: O 33 LYS cc_start: 0.9087 (mttt) cc_final: 0.8314 (mtmm) REVERT: O 49 SER cc_start: 0.9180 (m) cc_final: 0.8641 (t) REVERT: O 59 ASN cc_start: 0.8524 (m-40) cc_final: 0.7870 (m110) REVERT: O 69 LYS cc_start: 0.8065 (tttm) cc_final: 0.7529 (ttmt) REVERT: O 77 GLN cc_start: 0.8861 (tp-100) cc_final: 0.8540 (tp-100) REVERT: P 22 ASN cc_start: 0.9235 (p0) cc_final: 0.8556 (p0) REVERT: P 23 LEU cc_start: 0.8841 (tp) cc_final: 0.8403 (tt) REVERT: P 29 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: Q 25 THR cc_start: 0.8643 (m) cc_final: 0.8370 (p) REVERT: Q 40 ASP cc_start: 0.8134 (t0) cc_final: 0.7608 (t70) REVERT: Q 54 TYR cc_start: 0.8493 (t80) cc_final: 0.7974 (t80) REVERT: Q 69 LYS cc_start: 0.8359 (tttm) cc_final: 0.7867 (ttmt) REVERT: R 24 GLN cc_start: 0.8169 (mp10) cc_final: 0.7535 (pm20) REVERT: R 29 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8096 (tm-30) REVERT: R 59 ASN cc_start: 0.8620 (m-40) cc_final: 0.7446 (m110) REVERT: R 69 LYS cc_start: 0.8196 (tttm) cc_final: 0.6876 (mttt) REVERT: S 17 ASP cc_start: 0.7740 (m-30) cc_final: 0.7293 (m-30) REVERT: S 39 SER cc_start: 0.9302 (m) cc_final: 0.8406 (m) REVERT: S 58 ARG cc_start: 0.8939 (mmt180) cc_final: 0.8530 (mmt90) REVERT: S 59 ASN cc_start: 0.8680 (m-40) cc_final: 0.7539 (m110) REVERT: T 17 ASP cc_start: 0.8021 (m-30) cc_final: 0.7792 (m-30) REVERT: T 22 ASN cc_start: 0.8650 (p0) cc_final: 0.8238 (p0) REVERT: T 25 THR cc_start: 0.8541 (p) cc_final: 0.8075 (t) REVERT: T 39 SER cc_start: 0.9052 (m) cc_final: 0.8683 (p) REVERT: T 48 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8508 (tm-30) REVERT: T 50 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8601 (mmmt) REVERT: T 69 LYS cc_start: 0.6949 (tttm) cc_final: 0.6363 (tttt) outliers start: 31 outliers final: 27 residues processed: 567 average time/residue: 0.1083 time to fit residues: 87.8935 Evaluate side-chains 569 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 541 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN U 78 ASN M 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.092452 restraints weight = 17713.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095516 restraints weight = 9282.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097589 restraints weight = 5996.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099112 restraints weight = 4393.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100168 restraints weight = 3464.122| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11837 Z= 0.172 Angle : 0.570 8.114 16112 Z= 0.295 Chirality : 0.040 0.151 1843 Planarity : 0.003 0.016 2109 Dihedral : 3.677 26.017 1596 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.95 % Allowed : 26.32 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.22), residues: 1444 helix: 2.11 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.05 (0.39), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 58 TYR 0.029 0.002 TYR E 47 PHE 0.008 0.001 PHE O 16 TRP 0.011 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00403 (11837) covalent geometry : angle 0.56961 (16112) hydrogen bonds : bond 0.03250 ( 893) hydrogen bonds : angle 2.97370 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 549 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8692 (mmmt) REVERT: D 23 LEU cc_start: 0.8152 (tt) cc_final: 0.7932 (tp) REVERT: D 37 LYS cc_start: 0.8567 (ttmt) cc_final: 0.7622 (tptt) REVERT: U 15 LYS cc_start: 0.9073 (mttt) cc_final: 0.8829 (mmtp) REVERT: U 37 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7255 (tptt) REVERT: U 66 LYS cc_start: 0.8708 (tptp) cc_final: 0.6539 (mttt) REVERT: U 77 GLN cc_start: 0.8910 (tp40) cc_final: 0.8653 (tp40) REVERT: V 15 LYS cc_start: 0.9229 (tppp) cc_final: 0.9005 (mmtp) REVERT: V 37 LYS cc_start: 0.8765 (ttmt) cc_final: 0.7565 (tptt) REVERT: V 49 SER cc_start: 0.8650 (t) cc_final: 0.8250 (p) REVERT: V 77 GLN cc_start: 0.8737 (tp40) cc_final: 0.7921 (tp-100) REVERT: E 22 ASN cc_start: 0.8281 (p0) cc_final: 0.7694 (p0) REVERT: E 37 LYS cc_start: 0.8794 (ttmt) cc_final: 0.7621 (tptt) REVERT: E 66 LYS cc_start: 0.8365 (tptp) cc_final: 0.6812 (mttt) REVERT: F 34 LEU cc_start: 0.9246 (tp) cc_final: 0.8968 (tt) REVERT: F 37 LYS cc_start: 0.8693 (ttmt) cc_final: 0.7662 (tptt) REVERT: F 39 SER cc_start: 0.8859 (m) cc_final: 0.8209 (t) REVERT: F 47 TYR cc_start: 0.9048 (t80) cc_final: 0.8572 (t80) REVERT: F 49 SER cc_start: 0.9259 (t) cc_final: 0.8853 (p) REVERT: F 51 LEU cc_start: 0.9181 (tp) cc_final: 0.8924 (tp) REVERT: F 53 GLU cc_start: 0.8310 (tp30) cc_final: 0.7846 (mm-30) REVERT: F 66 LYS cc_start: 0.8612 (tptp) cc_final: 0.7588 (ttmt) REVERT: G 11 ASP cc_start: 0.8163 (m-30) cc_final: 0.7886 (t0) REVERT: G 15 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8752 (ttmm) REVERT: G 33 LYS cc_start: 0.9307 (mtpp) cc_final: 0.9075 (mtpp) REVERT: G 37 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7071 (tptt) REVERT: G 66 LYS cc_start: 0.8954 (tppt) cc_final: 0.8635 (tppt) REVERT: G 69 LYS cc_start: 0.8698 (tttm) cc_final: 0.8365 (tttt) REVERT: H 28 THR cc_start: 0.8971 (m) cc_final: 0.8430 (p) REVERT: H 32 ASP cc_start: 0.7890 (m-30) cc_final: 0.7597 (m-30) REVERT: H 37 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7037 (tptt) REVERT: H 47 TYR cc_start: 0.9067 (t80) cc_final: 0.7359 (t80) REVERT: H 51 LEU cc_start: 0.9290 (tp) cc_final: 0.8590 (tp) REVERT: H 54 TYR cc_start: 0.8987 (t80) cc_final: 0.8308 (t80) REVERT: I 37 LYS cc_start: 0.8686 (ttmt) cc_final: 0.7188 (tptp) REVERT: I 49 SER cc_start: 0.8926 (t) cc_final: 0.8690 (t) REVERT: I 76 ILE cc_start: 0.9740 (mm) cc_final: 0.9393 (tt) REVERT: I 78 ASN cc_start: 0.9305 (m-40) cc_final: 0.8959 (m-40) REVERT: J 22 ASN cc_start: 0.8344 (p0) cc_final: 0.7809 (p0) REVERT: J 24 GLN cc_start: 0.8258 (mp10) cc_final: 0.7877 (mp10) REVERT: J 37 LYS cc_start: 0.8759 (ttmt) cc_final: 0.7495 (tptt) REVERT: J 47 TYR cc_start: 0.9205 (t80) cc_final: 0.8529 (t80) REVERT: J 49 SER cc_start: 0.9250 (t) cc_final: 0.8966 (p) REVERT: K 33 LYS cc_start: 0.9274 (mttt) cc_final: 0.8868 (mtpp) REVERT: K 37 LYS cc_start: 0.8971 (ttmt) cc_final: 0.7518 (tptp) REVERT: K 47 TYR cc_start: 0.9043 (t80) cc_final: 0.7894 (t80) REVERT: K 63 ASN cc_start: 0.8630 (m-40) cc_final: 0.8392 (m110) REVERT: L 53 GLU cc_start: 0.8211 (tp30) cc_final: 0.7822 (tp30) REVERT: L 77 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8389 (tp40) REVERT: M 22 ASN cc_start: 0.8657 (p0) cc_final: 0.8314 (p0) REVERT: M 28 THR cc_start: 0.8767 (m) cc_final: 0.7972 (p) REVERT: M 31 LEU cc_start: 0.9320 (tp) cc_final: 0.8983 (tp) REVERT: M 32 ASP cc_start: 0.8385 (p0) cc_final: 0.8020 (p0) REVERT: M 47 TYR cc_start: 0.9143 (t80) cc_final: 0.8537 (t80) REVERT: M 66 LYS cc_start: 0.8538 (tptt) cc_final: 0.8029 (tmtt) REVERT: M 69 LYS cc_start: 0.8592 (tttp) cc_final: 0.7875 (ttpt) REVERT: N 24 GLN cc_start: 0.8573 (mp10) cc_final: 0.7795 (tm-30) REVERT: N 32 ASP cc_start: 0.8323 (m-30) cc_final: 0.8055 (m-30) REVERT: N 49 SER cc_start: 0.9430 (m) cc_final: 0.9171 (t) REVERT: N 50 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8459 (mmmt) REVERT: N 53 GLU cc_start: 0.8310 (tp30) cc_final: 0.7762 (tp30) REVERT: O 15 LYS cc_start: 0.8665 (tppt) cc_final: 0.8408 (tptp) REVERT: O 17 ASP cc_start: 0.8293 (m-30) cc_final: 0.7375 (t0) REVERT: O 22 ASN cc_start: 0.9178 (p0) cc_final: 0.8006 (p0) REVERT: O 25 THR cc_start: 0.9031 (m) cc_final: 0.8466 (p) REVERT: O 28 THR cc_start: 0.8463 (m) cc_final: 0.8119 (p) REVERT: O 33 LYS cc_start: 0.9101 (mttt) cc_final: 0.8339 (mtmm) REVERT: O 49 SER cc_start: 0.9181 (m) cc_final: 0.8681 (t) REVERT: O 59 ASN cc_start: 0.8547 (m-40) cc_final: 0.7914 (m110) REVERT: O 69 LYS cc_start: 0.8107 (tttm) cc_final: 0.7521 (ttmt) REVERT: O 77 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8551 (tp-100) REVERT: P 22 ASN cc_start: 0.9257 (p0) cc_final: 0.8715 (p0) REVERT: P 23 LEU cc_start: 0.8838 (tp) cc_final: 0.8425 (tt) REVERT: P 29 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: Q 25 THR cc_start: 0.8671 (m) cc_final: 0.8407 (p) REVERT: Q 40 ASP cc_start: 0.8201 (t0) cc_final: 0.7681 (t70) REVERT: Q 54 TYR cc_start: 0.8553 (t80) cc_final: 0.8046 (t80) REVERT: Q 69 LYS cc_start: 0.8404 (tttm) cc_final: 0.7911 (ttmt) REVERT: R 24 GLN cc_start: 0.8188 (mp10) cc_final: 0.7810 (pm20) REVERT: R 33 LYS cc_start: 0.9053 (mtmt) cc_final: 0.8833 (mtmm) REVERT: R 50 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8260 (mmmt) REVERT: R 59 ASN cc_start: 0.8621 (m-40) cc_final: 0.7473 (m110) REVERT: R 69 LYS cc_start: 0.8240 (tttm) cc_final: 0.6913 (mttt) REVERT: S 17 ASP cc_start: 0.7789 (m-30) cc_final: 0.7358 (m-30) REVERT: S 39 SER cc_start: 0.9333 (m) cc_final: 0.8431 (m) REVERT: S 58 ARG cc_start: 0.9031 (mmt180) cc_final: 0.8761 (mmt90) REVERT: S 59 ASN cc_start: 0.8725 (m-40) cc_final: 0.7557 (m110) REVERT: T 17 ASP cc_start: 0.8040 (m-30) cc_final: 0.7813 (m-30) REVERT: T 22 ASN cc_start: 0.8857 (p0) cc_final: 0.8472 (p0) REVERT: T 25 THR cc_start: 0.8583 (p) cc_final: 0.8120 (t) REVERT: T 39 SER cc_start: 0.9132 (m) cc_final: 0.8796 (p) REVERT: T 48 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8524 (tm-30) REVERT: T 50 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8537 (mmmt) REVERT: T 69 LYS cc_start: 0.6994 (tttm) cc_final: 0.6415 (tttt) outliers start: 37 outliers final: 34 residues processed: 562 average time/residue: 0.0959 time to fit residues: 77.5463 Evaluate side-chains 577 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 542 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 21 ASP Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 40 ASP Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain T residue 13 SER Chi-restraints excluded: chain T residue 33 LYS Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN D 77 GLN ** H 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN M 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.089669 restraints weight = 17724.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092646 restraints weight = 9417.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094718 restraints weight = 6145.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096134 restraints weight = 4534.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097179 restraints weight = 3627.155| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11837 Z= 0.224 Angle : 0.610 9.171 16112 Z= 0.316 Chirality : 0.042 0.156 1843 Planarity : 0.003 0.023 2109 Dihedral : 3.831 28.153 1596 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.27 % Allowed : 26.56 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.22), residues: 1444 helix: 2.02 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -3.98 (0.39), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG V 58 TYR 0.031 0.002 TYR E 47 PHE 0.011 0.001 PHE O 16 TRP 0.011 0.001 TRP R 5 Details of bonding type rmsd covalent geometry : bond 0.00523 (11837) covalent geometry : angle 0.61024 (16112) hydrogen bonds : bond 0.03479 ( 893) hydrogen bonds : angle 3.07819 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.71 seconds wall clock time: 36 minutes 8.93 seconds (2168.93 seconds total)