Starting phenix.real_space_refine on Tue Jul 29 06:50:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ofh_20046/07_2025/6ofh_20046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ofh_20046/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ofh_20046/07_2025/6ofh_20046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ofh_20046/07_2025/6ofh_20046.map" model { file = "/net/cci-nas-00/data/ceres_data/6ofh_20046/07_2025/6ofh_20046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ofh_20046/07_2025/6ofh_20046_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.023 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11628 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" 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: D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, V Time building chain proxies: 2.94, per 1000 atoms: 0.25 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: 2.52 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.89 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: 3.28 Time building geometry restraints manager: 3.07 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'V' } 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 23.500 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- 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 : 3.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.004 TRP G 5 PHE 0.020 0.004 PHE U 68 TYR 0.010 0.002 TYR D 57 ARG 0.004 0.001 ARG U 58 Details of bonding type rmsd hydrogen bonds : bond 0.26261 ( 893) hydrogen bonds : angle 9.46006 ( 2565) covalent geometry : bond 0.00794 (11837) covalent geometry : angle 0.75247 (16112) *********************** 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 : 1.468 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: 0.8488 (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: 0.7280 (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: 0.7499 (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: 0.9102 (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: 0.7287 (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: 0.8200 (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: 0.8766 (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: 0.7266 (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: 0.8021 (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: 0.8054 (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: 0.8715 (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: 0.8803 (t80) REVERT: N 31 LEU cc_start: 0.9170 (tp) cc_final: 0.8881 (tt) REVERT: N 43 LEU cc_start: 0.9280 (mt) cc_final: 0.8975 (mt) REVERT: N 47 TYR cc_start: 0.9145 (t80) cc_final: 0.8732 (t80) REVERT: N 51 LEU cc_start: 0.9065 (tp) cc_final: 0.8697 (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: 0.8390 (m) REVERT: O 28 THR cc_start: 0.8657 (m) cc_final: 0.8345 (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: 0.8834 (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: 0.8618 (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: 0.7707 (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: 0.7627 (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: 0.7824 (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: 0.8454 (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: 0.8107 (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: 0.6824 (mtt180) outliers start: 0 outliers final: 0 residues processed: 643 average time/residue: 0.2310 time to fit residues: 207.0536 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 : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3514 r_free = 0.3514 target = 0.122790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105856 restraints weight = 17194.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109248 restraints weight = 8849.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111517 restraints weight = 5613.608| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11837 Z= 0.151 Angle : 0.549 5.510 16112 Z= 0.304 Chirality : 0.037 0.134 1843 Planarity : 0.004 0.021 2109 Dihedral : 4.212 15.244 1596 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.87 % Allowed : 11.48 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 1444 helix: -0.77 (0.12), residues: 1292 sheet: None (None), residues: 0 loop : -5.28 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 5 PHE 0.010 0.001 PHE T 79 TYR 0.016 0.002 TYR O 54 ARG 0.005 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 893) hydrogen bonds : angle 3.37473 ( 2565) covalent geometry : bond 0.00319 (11837) covalent geometry : angle 0.54859 (16112) *********************** 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 617 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 581 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8205 (mmmt) REVERT: U 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8385 (mmmm) REVERT: U 37 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7175 (tptp) REVERT: U 53 GLU cc_start: 0.8408 (tp30) cc_final: 0.8078 (mm-30) REVERT: U 66 LYS cc_start: 0.8763 (tptp) cc_final: 0.6687 (mttt) REVERT: V 28 THR cc_start: 0.8706 (m) cc_final: 0.8290 (p) REVERT: V 37 LYS cc_start: 0.9253 (ttmt) cc_final: 0.7930 (tptt) REVERT: V 47 TYR cc_start: 0.8984 (t80) cc_final: 0.8205 (t80) REVERT: V 49 SER cc_start: 0.8631 (t) cc_final: 0.8292 (p) REVERT: V 53 GLU cc_start: 0.8402 (tp30) cc_final: 0.7961 (mm-30) REVERT: V 77 GLN cc_start: 0.8334 (tp40) cc_final: 0.7740 (tp-100) REVERT: E 32 ASP cc_start: 0.8125 (m-30) cc_final: 0.7883 (m-30) REVERT: E 37 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7036 (tptt) REVERT: E 48 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8548 (tm-30) REVERT: E 57 TYR cc_start: 0.8347 (t80) cc_final: 0.7847 (t80) REVERT: F 28 THR cc_start: 0.8720 (m) cc_final: 0.8209 (p) REVERT: F 32 ASP cc_start: 0.7712 (m-30) cc_final: 0.7434 (m-30) REVERT: F 34 LEU cc_start: 0.9246 (tp) cc_final: 0.8988 (tt) REVERT: F 37 LYS cc_start: 0.8620 (ttmt) cc_final: 0.7933 (tptt) REVERT: F 39 SER cc_start: 0.8687 (m) cc_final: 0.8290 (t) REVERT: F 47 TYR cc_start: 0.8910 (t80) cc_final: 0.8167 (t80) REVERT: F 49 SER cc_start: 0.9224 (t) cc_final: 0.8836 (p) REVERT: F 53 GLU cc_start: 0.8391 (tp30) cc_final: 0.7504 (mm-30) REVERT: F 66 LYS cc_start: 0.8883 (tptp) cc_final: 0.7315 (mttm) REVERT: G 11 ASP cc_start: 0.8377 (m-30) cc_final: 0.7834 (m-30) REVERT: G 15 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8880 (ttmm) REVERT: G 37 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7156 (tptt) REVERT: G 49 SER cc_start: 0.8772 (t) cc_final: 0.8221 (m) REVERT: G 69 LYS cc_start: 0.8586 (tttm) cc_final: 0.8358 (tttt) REVERT: H 28 THR cc_start: 0.8989 (m) cc_final: 0.8468 (p) REVERT: H 31 LEU cc_start: 0.8874 (tp) cc_final: 0.8608 (tt) REVERT: H 32 ASP cc_start: 0.8033 (m-30) cc_final: 0.7575 (m-30) REVERT: H 37 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7098 (tptt) REVERT: H 39 SER cc_start: 0.9132 (m) cc_final: 0.8887 (m) REVERT: H 47 TYR cc_start: 0.9168 (t80) cc_final: 0.7460 (t80) REVERT: H 51 LEU cc_start: 0.9255 (tp) cc_final: 0.8783 (tp) REVERT: I 28 THR cc_start: 0.9044 (m) cc_final: 0.8706 (p) REVERT: I 32 ASP cc_start: 0.8532 (m-30) cc_final: 0.8267 (m-30) REVERT: I 37 LYS cc_start: 0.8713 (ttmt) cc_final: 0.7315 (tptp) REVERT: I 47 TYR cc_start: 0.9269 (t80) cc_final: 0.8967 (t80) REVERT: I 49 SER cc_start: 0.9131 (t) cc_final: 0.8929 (t) REVERT: J 24 GLN cc_start: 0.8221 (mp10) cc_final: 0.7828 (tp-100) REVERT: J 37 LYS cc_start: 0.8779 (ttmt) cc_final: 0.7299 (tptp) REVERT: J 47 TYR cc_start: 0.9247 (t80) cc_final: 0.8692 (t80) REVERT: J 49 SER cc_start: 0.9261 (t) cc_final: 0.8803 (p) REVERT: J 50 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8717 (mmtt) REVERT: K 37 LYS cc_start: 0.9100 (ttmt) cc_final: 0.7778 (tptt) REVERT: K 40 ASP cc_start: 0.8096 (t0) cc_final: 0.7851 (t70) REVERT: K 47 TYR cc_start: 0.9153 (t80) cc_final: 0.8275 (t80) REVERT: K 50 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8863 (mmtp) REVERT: K 77 GLN cc_start: 0.8523 (tp40) cc_final: 0.8308 (tp-100) REVERT: L 23 LEU cc_start: 0.8804 (tp) cc_final: 0.8285 (tt) REVERT: L 26 GLN cc_start: 0.8512 (mt0) cc_final: 0.8279 (mt0) REVERT: L 31 LEU cc_start: 0.9150 (tp) cc_final: 0.8910 (tp) REVERT: L 37 LYS cc_start: 0.8751 (ttmt) cc_final: 0.7161 (tptt) REVERT: L 53 GLU cc_start: 0.8134 (tp30) cc_final: 0.7770 (tp30) REVERT: M 28 THR cc_start: 0.8762 (m) cc_final: 0.8318 (p) REVERT: M 31 LEU cc_start: 0.9095 (tp) cc_final: 0.8630 (tt) REVERT: M 32 ASP cc_start: 0.8395 (p0) cc_final: 0.8173 (p0) REVERT: M 39 SER cc_start: 0.9180 (m) cc_final: 0.8877 (p) REVERT: M 47 TYR cc_start: 0.9105 (t80) cc_final: 0.8635 (t80) REVERT: M 50 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8842 (mmtt) REVERT: M 66 LYS cc_start: 0.8756 (tptt) cc_final: 0.8170 (tmtt) REVERT: N 47 TYR cc_start: 0.8975 (t80) cc_final: 0.8554 (t80) REVERT: N 49 SER cc_start: 0.9617 (m) cc_final: 0.9335 (t) REVERT: N 50 LYS cc_start: 0.9264 (mmtp) cc_final: 0.8770 (mmmt) REVERT: N 51 LEU cc_start: 0.9043 (tp) cc_final: 0.8798 (tt) REVERT: N 53 GLU cc_start: 0.8303 (tp30) cc_final: 0.7795 (tp30) REVERT: N 58 ARG cc_start: 0.8423 (mmt180) cc_final: 0.8088 (mmt180) REVERT: O 17 ASP cc_start: 0.7900 (m-30) cc_final: 0.7149 (t0) REVERT: O 22 ASN cc_start: 0.9216 (p0) cc_final: 0.8369 (p0) REVERT: O 25 THR cc_start: 0.9065 (m) cc_final: 0.8714 (m) REVERT: O 28 THR cc_start: 0.8613 (m) cc_final: 0.7265 (p) REVERT: O 33 LYS cc_start: 0.9146 (mttt) cc_final: 0.8468 (mtmm) REVERT: O 47 TYR cc_start: 0.9129 (t80) cc_final: 0.8841 (t80) REVERT: O 49 SER cc_start: 0.9464 (m) cc_final: 0.9164 (t) REVERT: O 58 ARG cc_start: 0.8653 (mmt180) cc_final: 0.8376 (mmt-90) REVERT: O 59 ASN cc_start: 0.8555 (m-40) cc_final: 0.7838 (m110) REVERT: O 69 LYS cc_start: 0.8385 (tttm) cc_final: 0.7841 (tttt) REVERT: P 22 ASN cc_start: 0.9157 (p0) cc_final: 0.8879 (p0) REVERT: Q 28 THR cc_start: 0.8230 (m) cc_final: 0.7990 (p) REVERT: Q 40 ASP cc_start: 0.8351 (t0) cc_final: 0.7905 (t0) REVERT: Q 54 TYR cc_start: 0.8453 (t80) cc_final: 0.7872 (t80) REVERT: Q 57 TYR cc_start: 0.8984 (t80) cc_final: 0.8563 (t80) REVERT: Q 69 LYS cc_start: 0.8569 (tttm) cc_final: 0.8125 (ttmt) REVERT: Q 76 ILE cc_start: 0.8104 (mm) cc_final: 0.7842 (tt) REVERT: R 22 ASN cc_start: 0.8921 (p0) cc_final: 0.8169 (p0) REVERT: R 24 GLN cc_start: 0.8300 (mp10) cc_final: 0.8054 (pm20) REVERT: R 25 THR cc_start: 0.8612 (m) cc_final: 0.8083 (p) REVERT: R 29 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8028 (tm-30) REVERT: R 33 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8525 (mtmt) REVERT: R 39 SER cc_start: 0.9426 (m) cc_final: 0.9225 (t) REVERT: S 25 THR cc_start: 0.8161 (m) cc_final: 0.7810 (p) REVERT: S 39 SER cc_start: 0.8912 (m) cc_final: 0.8018 (m) REVERT: T 22 ASN cc_start: 0.8628 (p0) cc_final: 0.8096 (p0) REVERT: T 31 LEU cc_start: 0.8906 (tp) cc_final: 0.8658 (tp) REVERT: T 39 SER cc_start: 0.9085 (m) cc_final: 0.8776 (p) REVERT: T 40 ASP cc_start: 0.8328 (t0) cc_final: 0.7936 (t0) REVERT: T 48 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8813 (tm-30) REVERT: T 50 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8741 (mmmt) REVERT: T 66 LYS cc_start: 0.9030 (tptp) cc_final: 0.8688 (tppt) REVERT: T 69 LYS cc_start: 0.7037 (tttm) cc_final: 0.6656 (ttmt) outliers start: 36 outliers final: 24 residues processed: 594 average time/residue: 0.2357 time to fit residues: 196.5887 Evaluate side-chains 562 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 537 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 113 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 26 GLN S 26 GLN T 24 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101401 restraints weight = 17629.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104682 restraints weight = 9192.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106917 restraints weight = 5913.822| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3608 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= 0.156 Angle : 0.507 7.451 16112 Z= 0.271 Chirality : 0.037 0.113 1843 Planarity : 0.003 0.022 2109 Dihedral : 3.877 17.912 1596 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.83 % Allowed : 16.03 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1444 helix: 0.74 (0.13), residues: 1292 sheet: None (None), residues: 0 loop : -5.05 (0.25), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 5 PHE 0.007 0.001 PHE T 79 TYR 0.018 0.002 TYR N 57 ARG 0.004 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 893) hydrogen bonds : angle 3.07626 ( 2565) covalent geometry : bond 0.00345 (11837) covalent geometry : angle 0.50742 (16112) *********************** 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 611 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 563 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8342 (mmmt) REVERT: D 22 ASN cc_start: 0.7232 (p0) cc_final: 0.6937 (p0) REVERT: D 23 LEU cc_start: 0.7958 (tp) cc_final: 0.7561 (tt) REVERT: D 76 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.9015 (mt) REVERT: U 15 LYS cc_start: 0.8975 (mttt) cc_final: 0.8460 (mmmm) REVERT: U 37 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7244 (tptp) REVERT: U 66 LYS cc_start: 0.8743 (tptp) cc_final: 0.6656 (mttt) REVERT: V 37 LYS cc_start: 0.9185 (ttmt) cc_final: 0.7798 (tptt) REVERT: V 47 TYR cc_start: 0.9050 (t80) cc_final: 0.8302 (t80) REVERT: V 49 SER cc_start: 0.8613 (t) cc_final: 0.8268 (p) REVERT: V 53 GLU cc_start: 0.8081 (tp30) cc_final: 0.7873 (mm-30) REVERT: V 77 GLN cc_start: 0.8598 (tp40) cc_final: 0.7916 (tp-100) REVERT: E 11 ASP cc_start: 0.8127 (m-30) cc_final: 0.7637 (m-30) REVERT: E 15 LYS cc_start: 0.8450 (mttt) cc_final: 0.8175 (mtpp) REVERT: E 37 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7283 (tptt) REVERT: E 54 TYR cc_start: 0.8702 (t80) cc_final: 0.8416 (t80) REVERT: E 66 LYS cc_start: 0.8083 (tptp) cc_final: 0.6195 (mttt) REVERT: E 69 LYS cc_start: 0.7969 (tttm) cc_final: 0.7704 (tptp) REVERT: E 72 ASP cc_start: 0.8542 (m-30) cc_final: 0.8322 (t0) REVERT: F 28 THR cc_start: 0.8710 (m) cc_final: 0.8130 (p) REVERT: F 32 ASP cc_start: 0.7769 (m-30) cc_final: 0.7466 (m-30) REVERT: F 34 LEU cc_start: 0.9212 (tp) cc_final: 0.8934 (tt) REVERT: F 37 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7733 (tptt) REVERT: F 39 SER cc_start: 0.8775 (m) cc_final: 0.8225 (t) REVERT: F 47 TYR cc_start: 0.8891 (t80) cc_final: 0.8241 (t80) REVERT: F 49 SER cc_start: 0.9290 (t) cc_final: 0.8983 (p) REVERT: F 53 GLU cc_start: 0.8342 (tp30) cc_final: 0.7795 (mm-30) REVERT: F 66 LYS cc_start: 0.8841 (tptp) cc_final: 0.7355 (mttm) REVERT: G 11 ASP cc_start: 0.8403 (m-30) cc_final: 0.7973 (t0) REVERT: G 15 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8756 (ttmm) REVERT: G 37 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7078 (tptt) REVERT: G 69 LYS cc_start: 0.8733 (tttm) cc_final: 0.8418 (tttt) REVERT: H 23 LEU cc_start: 0.8866 (tp) cc_final: 0.8624 (tt) REVERT: H 28 THR cc_start: 0.8954 (m) cc_final: 0.8348 (p) REVERT: H 31 LEU cc_start: 0.8792 (tp) cc_final: 0.8567 (tt) REVERT: H 32 ASP cc_start: 0.7828 (m-30) cc_final: 0.7387 (m-30) REVERT: H 37 LYS cc_start: 0.8187 (ttmt) cc_final: 0.6997 (tptt) REVERT: H 47 TYR cc_start: 0.9153 (t80) cc_final: 0.7403 (t80) REVERT: H 51 LEU cc_start: 0.9313 (tp) cc_final: 0.8785 (tp) REVERT: H 77 GLN cc_start: 0.8557 (tp40) cc_final: 0.8347 (tp40) REVERT: I 28 THR cc_start: 0.9055 (m) cc_final: 0.8724 (p) REVERT: I 32 ASP cc_start: 0.8523 (m-30) cc_final: 0.8280 (m-30) REVERT: I 37 LYS cc_start: 0.8688 (ttmt) cc_final: 0.7304 (tptp) REVERT: I 47 TYR cc_start: 0.9282 (t80) cc_final: 0.8954 (t80) REVERT: I 49 SER cc_start: 0.9088 (t) cc_final: 0.8882 (t) REVERT: J 17 ASP cc_start: 0.7992 (m-30) cc_final: 0.7654 (m-30) REVERT: J 22 ASN cc_start: 0.8093 (p0) cc_final: 0.7527 (p0) REVERT: J 24 GLN cc_start: 0.7953 (mp10) cc_final: 0.7670 (tp-100) REVERT: J 37 LYS cc_start: 0.8780 (ttmt) cc_final: 0.7333 (tptt) REVERT: J 47 TYR cc_start: 0.9195 (t80) cc_final: 0.8631 (t80) REVERT: J 49 SER cc_start: 0.9245 (t) cc_final: 0.8870 (p) REVERT: K 33 LYS cc_start: 0.9189 (mttt) cc_final: 0.8810 (mtpp) REVERT: K 37 LYS cc_start: 0.9112 (ttmt) cc_final: 0.7752 (tptt) REVERT: K 47 TYR cc_start: 0.9155 (t80) cc_final: 0.7861 (t80) REVERT: K 63 ASN cc_start: 0.8627 (m-40) cc_final: 0.8398 (m110) REVERT: L 23 LEU cc_start: 0.8572 (tp) cc_final: 0.8250 (tt) REVERT: L 26 GLN cc_start: 0.8599 (mt0) cc_final: 0.8348 (tt0) REVERT: L 37 LYS cc_start: 0.8728 (ttmt) cc_final: 0.6969 (tptt) REVERT: L 48 GLN cc_start: 0.8620 (tt0) cc_final: 0.8033 (tt0) REVERT: L 53 GLU cc_start: 0.8146 (tp30) cc_final: 0.7843 (tp30) REVERT: M 28 THR cc_start: 0.8817 (m) cc_final: 0.8239 (p) REVERT: M 31 LEU cc_start: 0.9242 (tp) cc_final: 0.8738 (tt) REVERT: M 32 ASP cc_start: 0.8394 (p0) cc_final: 0.8117 (p0) REVERT: M 39 SER cc_start: 0.9125 (m) cc_final: 0.8589 (p) REVERT: M 47 TYR cc_start: 0.9255 (t80) cc_final: 0.8642 (t80) REVERT: M 66 LYS cc_start: 0.8807 (tptt) cc_final: 0.8140 (tmtt) REVERT: N 15 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8207 (ttmm) REVERT: N 24 GLN cc_start: 0.8791 (mp10) cc_final: 0.8123 (tm-30) REVERT: N 32 ASP cc_start: 0.8227 (m-30) cc_final: 0.8005 (m-30) REVERT: N 47 TYR cc_start: 0.8898 (t80) cc_final: 0.8569 (t80) REVERT: N 49 SER cc_start: 0.9533 (m) cc_final: 0.9276 (t) REVERT: N 50 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8461 (mmmt) REVERT: N 53 GLU cc_start: 0.8231 (tp30) cc_final: 0.7682 (tp30) REVERT: O 17 ASP cc_start: 0.7939 (m-30) cc_final: 0.7262 (t0) REVERT: O 22 ASN cc_start: 0.9240 (p0) cc_final: 0.7775 (p0) REVERT: O 25 THR cc_start: 0.9101 (m) cc_final: 0.8403 (p) REVERT: O 28 THR cc_start: 0.8438 (m) cc_final: 0.8119 (p) REVERT: O 33 LYS cc_start: 0.9135 (mttt) cc_final: 0.8431 (mtmm) REVERT: O 47 TYR cc_start: 0.9118 (t80) cc_final: 0.8683 (t80) REVERT: O 49 SER cc_start: 0.9317 (m) cc_final: 0.9024 (t) REVERT: O 52 SER cc_start: 0.9029 (m) cc_final: 0.8775 (t) REVERT: O 59 ASN cc_start: 0.8554 (m-40) cc_final: 0.7747 (m110) REVERT: O 69 LYS cc_start: 0.8124 (tttm) cc_final: 0.7835 (ttmt) REVERT: O 77 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8391 (tp-100) REVERT: P 22 ASN cc_start: 0.9234 (p0) cc_final: 0.8725 (p0) REVERT: P 24 GLN cc_start: 0.8204 (mp10) cc_final: 0.7968 (mp10) REVERT: P 26 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8953 (tt0) REVERT: P 56 LEU cc_start: 0.9307 (mt) cc_final: 0.9085 (mp) REVERT: Q 17 ASP cc_start: 0.7756 (m-30) cc_final: 0.7428 (m-30) REVERT: Q 25 THR cc_start: 0.8771 (m) cc_final: 0.8301 (p) REVERT: Q 28 THR cc_start: 0.8228 (m) cc_final: 0.7973 (p) REVERT: Q 40 ASP cc_start: 0.8238 (t0) cc_final: 0.7686 (t0) REVERT: Q 54 TYR cc_start: 0.8475 (t80) cc_final: 0.8016 (t80) REVERT: Q 57 TYR cc_start: 0.8917 (t80) cc_final: 0.8501 (t80) REVERT: Q 69 LYS cc_start: 0.8586 (tttm) cc_final: 0.8068 (ttmt) REVERT: R 22 ASN cc_start: 0.8951 (p0) cc_final: 0.8217 (p0) REVERT: R 24 GLN cc_start: 0.8329 (mp10) cc_final: 0.8106 (pm20) REVERT: R 33 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8625 (mtmt) REVERT: R 39 SER cc_start: 0.9333 (m) cc_final: 0.8994 (t) REVERT: S 25 THR cc_start: 0.8056 (m) cc_final: 0.7800 (p) REVERT: S 33 LYS cc_start: 0.8841 (mttp) cc_final: 0.8190 (mtpp) REVERT: S 39 SER cc_start: 0.9145 (m) cc_final: 0.8231 (m) REVERT: S 59 ASN cc_start: 0.8662 (m-40) cc_final: 0.8046 (m110) REVERT: S 76 ILE cc_start: 0.7906 (mt) cc_final: 0.7602 (tt) REVERT: T 22 ASN cc_start: 0.8651 (p0) cc_final: 0.8246 (p0) REVERT: T 25 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8152 (t) REVERT: T 48 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8826 (tm-30) REVERT: T 50 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8792 (mmmt) REVERT: T 69 LYS cc_start: 0.7105 (tttm) cc_final: 0.6594 (ttmt) outliers start: 48 outliers final: 31 residues processed: 578 average time/residue: 0.2184 time to fit residues: 178.2140 Evaluate side-chains 572 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 537 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain V residue 39 SER 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 G residue 15 LYS Chi-restraints excluded: chain I residue 21 ASP 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 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 38 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN ** O 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN T 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100967 restraints weight = 17500.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104213 restraints weight = 9201.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106395 restraints weight = 5929.506| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3952 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= 0.130 Angle : 0.476 6.390 16112 Z= 0.253 Chirality : 0.037 0.127 1843 Planarity : 0.003 0.018 2109 Dihedral : 3.698 18.713 1596 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.35 % Allowed : 19.22 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1444 helix: 1.40 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.91 (0.27), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 5 PHE 0.006 0.001 PHE N 68 TYR 0.013 0.001 TYR G 47 ARG 0.002 0.000 ARG J 80 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 893) hydrogen bonds : angle 2.93541 ( 2565) covalent geometry : bond 0.00288 (11837) covalent geometry : angle 0.47620 (16112) *********************** 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 602 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 560 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8374 (mmmt) REVERT: D 23 LEU cc_start: 0.7974 (tp) cc_final: 0.7657 (tt) REVERT: D 44 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8164 (mt) REVERT: U 15 LYS cc_start: 0.8999 (mttt) cc_final: 0.8522 (mmmm) REVERT: U 37 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7221 (tptp) REVERT: U 66 LYS cc_start: 0.8735 (tptp) cc_final: 0.6661 (mttp) REVERT: V 37 LYS cc_start: 0.9211 (ttmt) cc_final: 0.7849 (tptt) REVERT: V 40 ASP cc_start: 0.8448 (t0) cc_final: 0.8183 (t0) REVERT: V 43 LEU cc_start: 0.9238 (mt) cc_final: 0.8958 (mp) REVERT: V 47 TYR cc_start: 0.9065 (t80) cc_final: 0.8228 (t80) REVERT: V 49 SER cc_start: 0.8600 (t) cc_final: 0.8254 (p) REVERT: V 77 GLN cc_start: 0.8645 (tp40) cc_final: 0.7906 (tp-100) REVERT: E 11 ASP cc_start: 0.8476 (m-30) cc_final: 0.7853 (m-30) REVERT: E 23 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7068 (tp) REVERT: E 37 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7325 (tptt) REVERT: E 47 TYR cc_start: 0.8759 (t80) cc_final: 0.8284 (t80) REVERT: E 53 GLU cc_start: 0.8709 (tp30) cc_final: 0.8114 (mm-30) REVERT: E 66 LYS cc_start: 0.8234 (tptp) cc_final: 0.6666 (mttt) REVERT: E 69 LYS cc_start: 0.8093 (tttm) cc_final: 0.7844 (tptp) REVERT: F 28 THR cc_start: 0.8700 (m) cc_final: 0.8103 (p) REVERT: F 32 ASP cc_start: 0.7781 (m-30) cc_final: 0.7442 (m-30) REVERT: F 34 LEU cc_start: 0.9175 (tp) cc_final: 0.8908 (tt) REVERT: F 37 LYS cc_start: 0.8509 (ttmt) cc_final: 0.7778 (tptt) REVERT: F 39 SER cc_start: 0.8854 (m) cc_final: 0.8208 (t) REVERT: F 47 TYR cc_start: 0.8877 (t80) cc_final: 0.8268 (t80) REVERT: F 49 SER cc_start: 0.9309 (t) cc_final: 0.8938 (p) REVERT: F 53 GLU cc_start: 0.8290 (tp30) cc_final: 0.7757 (mm-30) REVERT: F 63 ASN cc_start: 0.9066 (m-40) cc_final: 0.8836 (m110) REVERT: F 66 LYS cc_start: 0.8839 (tptp) cc_final: 0.7313 (mttm) REVERT: G 11 ASP cc_start: 0.8377 (m-30) cc_final: 0.7981 (t0) REVERT: G 15 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8794 (ttmm) REVERT: G 33 LYS cc_start: 0.9314 (mtpp) cc_final: 0.9060 (mtpp) REVERT: G 37 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7222 (tptt) REVERT: G 69 LYS cc_start: 0.8749 (tttm) cc_final: 0.8426 (tttt) REVERT: H 23 LEU cc_start: 0.8876 (tp) cc_final: 0.8646 (tt) REVERT: H 28 THR cc_start: 0.8941 (m) cc_final: 0.8423 (p) REVERT: H 32 ASP cc_start: 0.7851 (m-30) cc_final: 0.7448 (m-30) REVERT: H 37 LYS cc_start: 0.8069 (ttmt) cc_final: 0.6872 (tptt) REVERT: H 47 TYR cc_start: 0.9136 (t80) cc_final: 0.7358 (t80) REVERT: H 51 LEU cc_start: 0.9329 (tp) cc_final: 0.8777 (tp) REVERT: H 54 TYR cc_start: 0.8915 (t80) cc_final: 0.8336 (t80) REVERT: H 56 LEU cc_start: 0.9298 (mt) cc_final: 0.9062 (mm) REVERT: H 77 GLN cc_start: 0.8579 (tp40) cc_final: 0.8366 (tp40) REVERT: I 28 THR cc_start: 0.9032 (m) cc_final: 0.8653 (p) REVERT: I 37 LYS cc_start: 0.8661 (ttmt) cc_final: 0.7280 (tptp) REVERT: I 47 TYR cc_start: 0.9284 (t80) cc_final: 0.8941 (t80) REVERT: J 17 ASP cc_start: 0.7978 (m-30) cc_final: 0.7675 (m-30) REVERT: J 22 ASN cc_start: 0.8165 (p0) cc_final: 0.7549 (p0) REVERT: J 37 LYS cc_start: 0.8785 (ttmt) cc_final: 0.7325 (tptt) REVERT: J 47 TYR cc_start: 0.9173 (t80) cc_final: 0.8630 (t80) REVERT: J 49 SER cc_start: 0.9230 (t) cc_final: 0.8832 (p) REVERT: J 57 TYR cc_start: 0.9220 (t80) cc_final: 0.8996 (t80) REVERT: K 33 LYS cc_start: 0.9200 (mttt) cc_final: 0.8850 (mtpp) REVERT: K 37 LYS cc_start: 0.9083 (ttmt) cc_final: 0.7706 (tptt) REVERT: K 47 TYR cc_start: 0.9146 (t80) cc_final: 0.7863 (t80) REVERT: K 63 ASN cc_start: 0.8617 (m-40) cc_final: 0.8316 (m-40) REVERT: L 23 LEU cc_start: 0.8625 (tp) cc_final: 0.8220 (tt) REVERT: L 26 GLN cc_start: 0.8605 (mt0) cc_final: 0.8363 (tt0) REVERT: L 37 LYS cc_start: 0.8801 (ttmt) cc_final: 0.7030 (tptt) REVERT: L 53 GLU cc_start: 0.8175 (tp30) cc_final: 0.7810 (tp30) REVERT: M 28 THR cc_start: 0.8826 (m) cc_final: 0.8129 (p) REVERT: M 31 LEU cc_start: 0.9278 (tp) cc_final: 0.8968 (tp) REVERT: M 32 ASP cc_start: 0.8334 (p0) cc_final: 0.7940 (p0) REVERT: M 39 SER cc_start: 0.9274 (m) cc_final: 0.8918 (p) REVERT: M 47 TYR cc_start: 0.9207 (t80) cc_final: 0.8585 (t80) REVERT: M 66 LYS cc_start: 0.8519 (tptt) cc_final: 0.8039 (tmtt) REVERT: N 15 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8174 (ttmm) REVERT: N 24 GLN cc_start: 0.8716 (mp10) cc_final: 0.7996 (tm-30) REVERT: N 32 ASP cc_start: 0.8229 (m-30) cc_final: 0.7989 (m-30) REVERT: N 47 TYR cc_start: 0.8897 (t80) cc_final: 0.8438 (t80) REVERT: N 49 SER cc_start: 0.9470 (m) cc_final: 0.9198 (t) REVERT: N 50 LYS cc_start: 0.8966 (mmtp) cc_final: 0.8453 (mmmt) REVERT: N 53 GLU cc_start: 0.8212 (tp30) cc_final: 0.7627 (tp30) REVERT: O 15 LYS cc_start: 0.8514 (tppp) cc_final: 0.8193 (tptp) REVERT: O 17 ASP cc_start: 0.7860 (m-30) cc_final: 0.7198 (t0) REVERT: O 22 ASN cc_start: 0.9216 (p0) cc_final: 0.7821 (p0) REVERT: O 25 THR cc_start: 0.9011 (m) cc_final: 0.8396 (p) REVERT: O 28 THR cc_start: 0.8297 (m) cc_final: 0.8046 (p) REVERT: O 33 LYS cc_start: 0.9137 (mttt) cc_final: 0.8397 (mtmm) REVERT: O 47 TYR cc_start: 0.9015 (t80) cc_final: 0.8759 (t80) REVERT: O 49 SER cc_start: 0.9249 (m) cc_final: 0.8994 (t) REVERT: O 52 SER cc_start: 0.8979 (m) cc_final: 0.8668 (t) REVERT: O 59 ASN cc_start: 0.8489 (m-40) cc_final: 0.7707 (m110) REVERT: O 69 LYS cc_start: 0.8145 (tttm) cc_final: 0.7821 (ttmt) REVERT: O 77 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8396 (tp-100) REVERT: P 22 ASN cc_start: 0.9257 (p0) cc_final: 0.8858 (p0) REVERT: P 40 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7653 (p0) REVERT: Q 25 THR cc_start: 0.8795 (m) cc_final: 0.8195 (p) REVERT: Q 31 LEU cc_start: 0.8823 (tp) cc_final: 0.8603 (tp) REVERT: Q 40 ASP cc_start: 0.8239 (t0) cc_final: 0.8006 (t0) REVERT: Q 54 TYR cc_start: 0.8471 (t80) cc_final: 0.7882 (t80) REVERT: Q 57 TYR cc_start: 0.9009 (t80) cc_final: 0.8588 (t80) REVERT: Q 69 LYS cc_start: 0.8286 (tttm) cc_final: 0.7670 (tttp) REVERT: R 22 ASN cc_start: 0.9062 (p0) cc_final: 0.8543 (p0) REVERT: R 24 GLN cc_start: 0.8235 (mp10) cc_final: 0.7853 (pm20) REVERT: R 29 GLU cc_start: 0.8651 (tm-30) cc_final: 0.7986 (tm-30) REVERT: R 39 SER cc_start: 0.9363 (m) cc_final: 0.9020 (t) REVERT: S 39 SER cc_start: 0.9195 (m) cc_final: 0.8308 (m) REVERT: S 59 ASN cc_start: 0.8663 (m-40) cc_final: 0.7695 (m110) REVERT: S 69 LYS cc_start: 0.7681 (tttm) cc_final: 0.7379 (ttmt) REVERT: T 22 ASN cc_start: 0.8693 (p0) cc_final: 0.8316 (p0) REVERT: T 25 THR cc_start: 0.8650 (p) cc_final: 0.8154 (t) REVERT: T 48 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8431 (tm-30) REVERT: T 50 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8705 (mmtt) REVERT: T 69 LYS cc_start: 0.7132 (tttm) cc_final: 0.6583 (ttmt) outliers start: 42 outliers final: 30 residues processed: 570 average time/residue: 0.2127 time to fit residues: 172.6667 Evaluate side-chains 573 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 540 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 52 SER 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 I residue 25 THR 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 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 34 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 33 LYS Chi-restraints excluded: chain P residue 40 ASP 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 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 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 61 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.0000 overall best weight: 1.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN O 55 ASN T 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099073 restraints weight = 17373.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102301 restraints weight = 9119.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104465 restraints weight = 5880.718| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11837 Z= 0.117 Angle : 0.476 7.472 16112 Z= 0.249 Chirality : 0.036 0.143 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.556 23.162 1596 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.35 % Allowed : 21.13 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1444 helix: 1.82 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.68 (0.30), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 5 PHE 0.005 0.001 PHE L 79 TYR 0.012 0.001 TYR G 47 ARG 0.002 0.000 ARG O 58 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 893) hydrogen bonds : angle 2.87936 ( 2565) covalent geometry : bond 0.00257 (11837) covalent geometry : angle 0.47647 (16112) *********************** 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 597 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 555 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8383 (mmmt) REVERT: D 22 ASN cc_start: 0.7653 (p0) cc_final: 0.7259 (p0) REVERT: D 28 THR cc_start: 0.8403 (m) cc_final: 0.8171 (p) REVERT: D 44 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8181 (mt) REVERT: U 15 LYS cc_start: 0.8998 (mttt) cc_final: 0.8544 (ttmt) REVERT: U 22 ASN cc_start: 0.8137 (p0) cc_final: 0.7884 (p0) REVERT: U 37 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7154 (tptp) REVERT: U 66 LYS cc_start: 0.8716 (tptp) cc_final: 0.6611 (mttp) REVERT: V 37 LYS cc_start: 0.9183 (ttmt) cc_final: 0.7849 (tptt) REVERT: V 40 ASP cc_start: 0.8425 (t0) cc_final: 0.8096 (t70) REVERT: V 43 LEU cc_start: 0.9226 (mt) cc_final: 0.8821 (mp) REVERT: V 47 TYR cc_start: 0.9069 (t80) cc_final: 0.8226 (t80) REVERT: V 49 SER cc_start: 0.8567 (t) cc_final: 0.8217 (p) REVERT: V 77 GLN cc_start: 0.8683 (tp40) cc_final: 0.7936 (tp-100) REVERT: E 32 ASP cc_start: 0.8088 (m-30) cc_final: 0.7860 (m-30) REVERT: E 37 LYS cc_start: 0.8700 (ttmt) cc_final: 0.7425 (tptt) REVERT: E 47 TYR cc_start: 0.8709 (t80) cc_final: 0.8304 (t80) REVERT: E 53 GLU cc_start: 0.8683 (tp30) cc_final: 0.8226 (mm-30) REVERT: E 66 LYS cc_start: 0.8239 (tptp) cc_final: 0.6712 (mttt) REVERT: E 69 LYS cc_start: 0.8282 (tttm) cc_final: 0.7914 (tptp) REVERT: F 28 THR cc_start: 0.8683 (m) cc_final: 0.8073 (p) REVERT: F 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7428 (m-30) REVERT: F 34 LEU cc_start: 0.9162 (tp) cc_final: 0.8889 (tt) REVERT: F 37 LYS cc_start: 0.8528 (ttmt) cc_final: 0.7838 (tptt) REVERT: F 39 SER cc_start: 0.8862 (m) cc_final: 0.8259 (t) REVERT: F 47 TYR cc_start: 0.8904 (t80) cc_final: 0.8285 (t80) REVERT: F 49 SER cc_start: 0.9225 (t) cc_final: 0.8825 (p) REVERT: F 53 GLU cc_start: 0.8286 (tp30) cc_final: 0.7617 (mm-30) REVERT: F 63 ASN cc_start: 0.9031 (m-40) cc_final: 0.8751 (m110) REVERT: F 66 LYS cc_start: 0.8658 (tptp) cc_final: 0.7682 (ttmt) REVERT: G 8 TYR cc_start: 0.8629 (t80) cc_final: 0.8107 (t80) REVERT: G 11 ASP cc_start: 0.8199 (m-30) cc_final: 0.7900 (t0) REVERT: G 15 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8735 (ttmm) REVERT: G 33 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9074 (mtpp) REVERT: G 37 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7135 (tptt) REVERT: G 69 LYS cc_start: 0.8707 (tttm) cc_final: 0.8423 (tttt) REVERT: H 23 LEU cc_start: 0.8832 (tp) cc_final: 0.8612 (tt) REVERT: H 37 LYS cc_start: 0.8236 (ttmt) cc_final: 0.6967 (tptt) REVERT: H 47 TYR cc_start: 0.9064 (t80) cc_final: 0.7329 (t80) REVERT: H 51 LEU cc_start: 0.9347 (tp) cc_final: 0.8763 (tp) REVERT: H 54 TYR cc_start: 0.8892 (t80) cc_final: 0.8069 (t80) REVERT: I 37 LYS cc_start: 0.8649 (ttmt) cc_final: 0.7119 (tptp) REVERT: I 47 TYR cc_start: 0.9262 (t80) cc_final: 0.8935 (t80) REVERT: I 77 GLN cc_start: 0.8562 (tp40) cc_final: 0.8331 (tp40) REVERT: J 17 ASP cc_start: 0.7917 (m-30) cc_final: 0.7677 (m-30) REVERT: J 22 ASN cc_start: 0.7977 (p0) cc_final: 0.7401 (p0) REVERT: J 24 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7372 (tp-100) REVERT: J 37 LYS cc_start: 0.8755 (ttmt) cc_final: 0.7289 (tptt) REVERT: J 47 TYR cc_start: 0.9149 (t80) cc_final: 0.8573 (t80) REVERT: J 49 SER cc_start: 0.9260 (t) cc_final: 0.8970 (p) REVERT: J 57 TYR cc_start: 0.9246 (t80) cc_final: 0.8871 (t80) REVERT: J 80 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7538 (ttp80) REVERT: K 33 LYS cc_start: 0.9212 (mttt) cc_final: 0.8833 (mtpp) REVERT: K 37 LYS cc_start: 0.8990 (ttmt) cc_final: 0.7501 (tptt) REVERT: K 47 TYR cc_start: 0.9128 (t80) cc_final: 0.7744 (t80) REVERT: K 63 ASN cc_start: 0.8605 (m-40) cc_final: 0.8071 (m110) REVERT: L 23 LEU cc_start: 0.8659 (tp) cc_final: 0.8424 (tt) REVERT: L 26 GLN cc_start: 0.8622 (mt0) cc_final: 0.8268 (tt0) REVERT: L 53 GLU cc_start: 0.8169 (tp30) cc_final: 0.7861 (tp30) REVERT: L 77 GLN cc_start: 0.8395 (tp-100) cc_final: 0.8013 (tp40) REVERT: M 28 THR cc_start: 0.8800 (m) cc_final: 0.8092 (p) REVERT: M 31 LEU cc_start: 0.9302 (tp) cc_final: 0.8997 (tp) REVERT: M 32 ASP cc_start: 0.8344 (p0) cc_final: 0.7943 (p0) REVERT: M 47 TYR cc_start: 0.9194 (t80) cc_final: 0.8547 (t80) REVERT: M 66 LYS cc_start: 0.8548 (tptt) cc_final: 0.8019 (tmtt) REVERT: N 24 GLN cc_start: 0.8631 (mp10) cc_final: 0.7803 (tm-30) REVERT: N 32 ASP cc_start: 0.8276 (m-30) cc_final: 0.8027 (m-30) REVERT: N 49 SER cc_start: 0.9428 (m) cc_final: 0.9105 (t) REVERT: N 53 GLU cc_start: 0.8208 (tp30) cc_final: 0.7595 (tp30) REVERT: O 17 ASP cc_start: 0.8130 (m-30) cc_final: 0.7416 (t0) REVERT: O 22 ASN cc_start: 0.9210 (p0) cc_final: 0.7936 (p0) REVERT: O 25 THR cc_start: 0.8992 (m) cc_final: 0.8403 (p) REVERT: O 28 THR cc_start: 0.8382 (m) cc_final: 0.8073 (p) REVERT: O 33 LYS cc_start: 0.9122 (mttt) cc_final: 0.8423 (mtmm) REVERT: O 47 TYR cc_start: 0.8993 (t80) cc_final: 0.8721 (t80) REVERT: O 49 SER cc_start: 0.9179 (m) cc_final: 0.8912 (t) REVERT: O 52 SER cc_start: 0.8840 (m) cc_final: 0.8595 (t) REVERT: O 59 ASN cc_start: 0.8463 (m-40) cc_final: 0.7795 (m110) REVERT: O 69 LYS cc_start: 0.8301 (tttm) cc_final: 0.7765 (ttmt) REVERT: O 77 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8516 (tp-100) REVERT: P 22 ASN cc_start: 0.9255 (p0) cc_final: 0.8834 (p0) REVERT: P 23 LEU cc_start: 0.8885 (tp) cc_final: 0.8474 (tt) REVERT: P 40 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8021 (p0) REVERT: P 69 LYS cc_start: 0.8215 (tttm) cc_final: 0.7676 (ttmt) REVERT: Q 25 THR cc_start: 0.8672 (m) cc_final: 0.8391 (p) REVERT: Q 40 ASP cc_start: 0.8095 (t0) cc_final: 0.7825 (t0) REVERT: Q 54 TYR cc_start: 0.8486 (t80) cc_final: 0.7856 (t80) REVERT: Q 57 TYR cc_start: 0.8837 (t80) cc_final: 0.8554 (t80) REVERT: Q 69 LYS cc_start: 0.8354 (tttm) cc_final: 0.7703 (tttp) REVERT: R 17 ASP cc_start: 0.7364 (m-30) cc_final: 0.7155 (m-30) REVERT: R 22 ASN cc_start: 0.9019 (p0) cc_final: 0.8593 (p0) REVERT: R 24 GLN cc_start: 0.8187 (mp10) cc_final: 0.7828 (pm20) REVERT: R 29 GLU cc_start: 0.8508 (tm-30) cc_final: 0.7897 (tm-30) REVERT: R 39 SER cc_start: 0.9368 (m) cc_final: 0.8980 (t) REVERT: R 51 LEU cc_start: 0.9249 (tp) cc_final: 0.8605 (tt) REVERT: S 17 ASP cc_start: 0.7006 (m-30) cc_final: 0.6700 (m-30) REVERT: S 33 LYS cc_start: 0.8825 (mttp) cc_final: 0.8236 (mtmt) REVERT: S 39 SER cc_start: 0.9198 (m) cc_final: 0.8273 (m) REVERT: S 59 ASN cc_start: 0.8671 (m-40) cc_final: 0.7648 (m110) REVERT: S 69 LYS cc_start: 0.7701 (tttm) cc_final: 0.7341 (ttmt) REVERT: T 22 ASN cc_start: 0.8857 (p0) cc_final: 0.8471 (p0) REVERT: T 25 THR cc_start: 0.8655 (p) cc_final: 0.8390 (p) REVERT: T 48 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8461 (tm-30) REVERT: T 69 LYS cc_start: 0.6822 (tttm) cc_final: 0.6252 (tttt) outliers start: 42 outliers final: 28 residues processed: 564 average time/residue: 0.2182 time to fit residues: 176.3870 Evaluate side-chains 571 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 540 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 76 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 15 LYS Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 31 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 K residue 67 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain M residue 80 ARG Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR 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 40 ASP Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU 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 22 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 93 optimal weight: 2.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- 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** M 26 GLN M 77 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.092238 restraints weight = 17615.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095342 restraints weight = 9155.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097516 restraints weight = 5890.049| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11837 Z= 0.143 Angle : 0.503 7.449 16112 Z= 0.263 Chirality : 0.038 0.127 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.579 23.537 1596 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.99 % Allowed : 22.01 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.22), residues: 1444 helix: 1.96 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.45 (0.34), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 5 PHE 0.006 0.001 PHE N 68 TYR 0.012 0.002 TYR R 57 ARG 0.002 0.000 ARG V 58 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 893) hydrogen bonds : angle 2.94227 ( 2565) covalent geometry : bond 0.00328 (11837) covalent geometry : angle 0.50270 (16112) *********************** 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 605 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 555 time to evaluate : 1.255 Fit side-chains REVERT: D 15 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8401 (mmmt) REVERT: D 22 ASN cc_start: 0.7928 (p0) cc_final: 0.7555 (p0) REVERT: D 44 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7649 (mt) REVERT: D 63 ASN cc_start: 0.7918 (m-40) cc_final: 0.7400 (m-40) REVERT: U 15 LYS cc_start: 0.9105 (mttt) cc_final: 0.8803 (mmtp) REVERT: U 22 ASN cc_start: 0.8280 (p0) cc_final: 0.8045 (p0) REVERT: U 37 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7204 (tptp) REVERT: U 66 LYS cc_start: 0.8723 (tptp) cc_final: 0.6640 (mttp) REVERT: V 37 LYS cc_start: 0.8647 (ttmt) cc_final: 0.7573 (tptt) REVERT: V 43 LEU cc_start: 0.9232 (mt) cc_final: 0.8807 (mp) REVERT: V 47 TYR cc_start: 0.9121 (t80) cc_final: 0.8320 (t80) REVERT: V 49 SER cc_start: 0.8655 (t) cc_final: 0.8296 (p) REVERT: V 77 GLN cc_start: 0.8730 (tp40) cc_final: 0.8220 (tp40) REVERT: E 15 LYS cc_start: 0.8757 (mmmm) cc_final: 0.8506 (mmmt) REVERT: E 22 ASN cc_start: 0.7566 (p0) cc_final: 0.6786 (p0) REVERT: E 32 ASP cc_start: 0.7992 (m-30) cc_final: 0.7619 (m-30) REVERT: E 37 LYS cc_start: 0.8696 (ttmt) cc_final: 0.7480 (tptt) REVERT: E 47 TYR cc_start: 0.8911 (t80) cc_final: 0.8596 (t80) REVERT: E 53 GLU cc_start: 0.8634 (tp30) cc_final: 0.8207 (mm-30) REVERT: E 66 LYS cc_start: 0.8330 (tptp) cc_final: 0.6873 (mttt) REVERT: F 28 THR cc_start: 0.8708 (m) cc_final: 0.8092 (p) REVERT: F 32 ASP cc_start: 0.7746 (m-30) cc_final: 0.7413 (m-30) REVERT: F 34 LEU cc_start: 0.9203 (tp) cc_final: 0.8931 (tt) REVERT: F 37 LYS cc_start: 0.8501 (ttmt) cc_final: 0.7827 (tptt) REVERT: F 39 SER cc_start: 0.8875 (m) cc_final: 0.8197 (t) REVERT: F 47 TYR cc_start: 0.8960 (t80) cc_final: 0.8353 (t80) REVERT: F 49 SER cc_start: 0.9243 (t) cc_final: 0.8851 (p) REVERT: F 53 GLU cc_start: 0.8277 (tp30) cc_final: 0.7714 (mm-30) REVERT: F 63 ASN cc_start: 0.9079 (m-40) cc_final: 0.8797 (m110) REVERT: F 66 LYS cc_start: 0.8671 (tptp) cc_final: 0.7337 (mttm) REVERT: G 11 ASP cc_start: 0.8220 (m-30) cc_final: 0.7917 (t0) REVERT: G 15 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8675 (ttmm) REVERT: G 33 LYS cc_start: 0.9327 (mtpp) cc_final: 0.9073 (mtpp) REVERT: G 37 LYS cc_start: 0.8463 (ttmt) cc_final: 0.7208 (tptt) REVERT: G 66 LYS cc_start: 0.9064 (tppt) cc_final: 0.8561 (tppt) REVERT: G 69 LYS cc_start: 0.8710 (tttm) cc_final: 0.8400 (tttt) REVERT: H 23 LEU cc_start: 0.8864 (tp) cc_final: 0.8625 (tt) REVERT: H 32 ASP cc_start: 0.7757 (m-30) cc_final: 0.7475 (m-30) REVERT: H 37 LYS cc_start: 0.8270 (ttmt) cc_final: 0.6945 (tptt) REVERT: H 47 TYR cc_start: 0.9109 (t80) cc_final: 0.7381 (t80) REVERT: H 51 LEU cc_start: 0.9342 (tp) cc_final: 0.8779 (tp) REVERT: H 54 TYR cc_start: 0.8889 (t80) cc_final: 0.8484 (t80) REVERT: I 37 LYS cc_start: 0.8657 (ttmt) cc_final: 0.7106 (tptp) REVERT: I 47 TYR cc_start: 0.9204 (t80) cc_final: 0.8896 (t80) REVERT: I 77 GLN cc_start: 0.8654 (tp40) cc_final: 0.8443 (tp40) REVERT: J 17 ASP cc_start: 0.7937 (m-30) cc_final: 0.7645 (m-30) REVERT: J 22 ASN cc_start: 0.8074 (p0) cc_final: 0.7521 (p0) REVERT: J 24 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7182 (tp-100) REVERT: J 37 LYS cc_start: 0.8771 (ttmt) cc_final: 0.7392 (tptt) REVERT: J 47 TYR cc_start: 0.9163 (t80) cc_final: 0.8481 (t80) REVERT: J 49 SER cc_start: 0.9282 (t) cc_final: 0.8945 (p) REVERT: J 80 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7499 (ttp80) REVERT: K 15 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8768 (tptm) REVERT: K 33 LYS cc_start: 0.9219 (mttt) cc_final: 0.8848 (mtpp) REVERT: K 37 LYS cc_start: 0.8991 (ttmt) cc_final: 0.7558 (tptp) REVERT: K 47 TYR cc_start: 0.9142 (t80) cc_final: 0.7763 (t80) REVERT: K 63 ASN cc_start: 0.8671 (m-40) cc_final: 0.8253 (m-40) REVERT: L 26 GLN cc_start: 0.8809 (mt0) cc_final: 0.8395 (tt0) REVERT: L 48 GLN cc_start: 0.8448 (tt0) cc_final: 0.7814 (tt0) REVERT: L 53 GLU cc_start: 0.8212 (tp30) cc_final: 0.7834 (tp30) REVERT: L 77 GLN cc_start: 0.8476 (tp-100) cc_final: 0.8082 (tp40) REVERT: M 22 ASN cc_start: 0.8483 (p0) cc_final: 0.8110 (p0) REVERT: M 26 GLN cc_start: 0.8824 (mt0) cc_final: 0.8587 (mt0) REVERT: M 28 THR cc_start: 0.8822 (m) cc_final: 0.8083 (p) REVERT: M 31 LEU cc_start: 0.9280 (tp) cc_final: 0.8959 (tp) REVERT: M 32 ASP cc_start: 0.8405 (p0) cc_final: 0.8046 (p0) REVERT: M 47 TYR cc_start: 0.9286 (t80) cc_final: 0.8691 (t80) REVERT: M 66 LYS cc_start: 0.8582 (tptt) cc_final: 0.8066 (tmtt) REVERT: N 24 GLN cc_start: 0.8630 (mp10) cc_final: 0.7763 (tm-30) REVERT: N 32 ASP cc_start: 0.8293 (m-30) cc_final: 0.8047 (m-30) REVERT: N 49 SER cc_start: 0.9418 (m) cc_final: 0.9094 (t) REVERT: N 53 GLU cc_start: 0.8225 (tp30) cc_final: 0.7627 (tp30) REVERT: O 17 ASP cc_start: 0.8179 (m-30) cc_final: 0.7463 (t0) REVERT: O 22 ASN cc_start: 0.9205 (p0) cc_final: 0.8015 (p0) REVERT: O 25 THR cc_start: 0.8989 (m) cc_final: 0.8380 (p) REVERT: O 28 THR cc_start: 0.8394 (m) cc_final: 0.8107 (p) REVERT: O 33 LYS cc_start: 0.9131 (mttt) cc_final: 0.8433 (mtmm) REVERT: O 49 SER cc_start: 0.9187 (m) cc_final: 0.8904 (t) REVERT: O 52 SER cc_start: 0.8995 (m) cc_final: 0.8785 (t) REVERT: O 59 ASN cc_start: 0.8551 (m-40) cc_final: 0.7804 (m110) REVERT: O 69 LYS cc_start: 0.8214 (tttm) cc_final: 0.7694 (ttmt) REVERT: O 77 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8590 (tp-100) REVERT: P 21 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8136 (t0) REVERT: P 22 ASN cc_start: 0.9304 (p0) cc_final: 0.8739 (p0) REVERT: P 23 LEU cc_start: 0.8897 (tp) cc_final: 0.8425 (tt) REVERT: P 29 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: P 40 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.7935 (p0) REVERT: Q 25 THR cc_start: 0.8659 (m) cc_final: 0.8402 (p) REVERT: Q 40 ASP cc_start: 0.8137 (t0) cc_final: 0.7864 (t0) REVERT: Q 49 SER cc_start: 0.9235 (m) cc_final: 0.8716 (t) REVERT: Q 54 TYR cc_start: 0.8561 (t80) cc_final: 0.7902 (t80) REVERT: Q 69 LYS cc_start: 0.8388 (tttm) cc_final: 0.7704 (tttp) REVERT: R 17 ASP cc_start: 0.7628 (m-30) cc_final: 0.7344 (m-30) REVERT: R 22 ASN cc_start: 0.9087 (p0) cc_final: 0.8681 (p0) REVERT: R 24 GLN cc_start: 0.8164 (mp10) cc_final: 0.7871 (pm20) REVERT: R 39 SER cc_start: 0.9386 (m) cc_final: 0.9041 (t) REVERT: R 51 LEU cc_start: 0.9100 (tp) cc_final: 0.8656 (tt) REVERT: R 69 LYS cc_start: 0.8185 (tttm) cc_final: 0.7135 (mttt) REVERT: S 17 ASP cc_start: 0.7173 (m-30) cc_final: 0.6863 (m-30) REVERT: S 31 LEU cc_start: 0.8870 (tp) cc_final: 0.8610 (tp) REVERT: S 33 LYS cc_start: 0.8847 (mttp) cc_final: 0.8266 (mtmt) REVERT: S 39 SER cc_start: 0.9271 (m) cc_final: 0.8376 (m) REVERT: S 59 ASN cc_start: 0.8674 (m-40) cc_final: 0.7658 (m110) REVERT: S 69 LYS cc_start: 0.7701 (tttm) cc_final: 0.7350 (ttmt) REVERT: T 22 ASN cc_start: 0.8676 (p0) cc_final: 0.8305 (p0) REVERT: T 25 THR cc_start: 0.8666 (p) cc_final: 0.8146 (t) REVERT: T 48 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8462 (tm-30) REVERT: T 50 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8693 (mmmt) REVERT: T 69 LYS cc_start: 0.6932 (tttm) cc_final: 0.6338 (tttt) outliers start: 50 outliers final: 38 residues processed: 566 average time/residue: 0.2160 time to fit residues: 174.8750 Evaluate side-chains 583 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 541 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 LEU 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 12 VAL 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 N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR 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 21 ASP Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 40 ASP Chi-restraints excluded: chain P residue 53 GLU 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 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 67 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 64 THR Chi-restraints excluded: chain T residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** H 77 GLN M 77 GLN S 26 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.095626 restraints weight = 18055.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098768 restraints weight = 9591.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100910 restraints weight = 6237.562| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11837 Z= 0.216 Angle : 0.573 9.543 16112 Z= 0.299 Chirality : 0.041 0.202 1843 Planarity : 0.003 0.021 2109 Dihedral : 3.809 27.872 1596 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.86 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1444 helix: 1.92 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.23 (0.36), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 5 PHE 0.012 0.002 PHE M 79 TYR 0.019 0.002 TYR Q 57 ARG 0.004 0.001 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 893) hydrogen bonds : angle 3.06800 ( 2565) covalent geometry : bond 0.00496 (11837) covalent geometry : angle 0.57330 (16112) *********************** 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 628 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 567 time to evaluate : 1.306 Fit side-chains REVERT: D 15 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8486 (mmmt) REVERT: D 44 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 56 LEU cc_start: 0.8968 (mt) cc_final: 0.8677 (mt) REVERT: D 66 LYS cc_start: 0.9244 (tptp) cc_final: 0.7496 (mttt) REVERT: U 15 LYS cc_start: 0.9126 (mttt) cc_final: 0.8860 (mmtp) REVERT: U 22 ASN cc_start: 0.8477 (p0) cc_final: 0.8231 (p0) REVERT: U 37 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7208 (tptt) REVERT: U 66 LYS cc_start: 0.8665 (tptp) cc_final: 0.7010 (mttt) REVERT: V 37 LYS cc_start: 0.8760 (ttmt) cc_final: 0.7540 (tptt) REVERT: V 47 TYR cc_start: 0.9221 (t80) cc_final: 0.8162 (t80) REVERT: V 49 SER cc_start: 0.8627 (t) cc_final: 0.8274 (p) REVERT: V 77 GLN cc_start: 0.8724 (tp40) cc_final: 0.7859 (tp-100) REVERT: E 22 ASN cc_start: 0.8013 (p0) cc_final: 0.7274 (p0) REVERT: E 32 ASP cc_start: 0.8081 (m-30) cc_final: 0.7679 (m-30) REVERT: E 37 LYS cc_start: 0.8713 (ttmt) cc_final: 0.7399 (tptt) REVERT: E 53 GLU cc_start: 0.8620 (tp30) cc_final: 0.8209 (mm-30) REVERT: E 66 LYS cc_start: 0.8373 (tptp) cc_final: 0.6937 (mttt) REVERT: E 69 LYS cc_start: 0.8530 (tttp) cc_final: 0.8300 (tttp) REVERT: F 28 THR cc_start: 0.8728 (m) cc_final: 0.8108 (p) REVERT: F 32 ASP cc_start: 0.7799 (m-30) cc_final: 0.7480 (m-30) REVERT: F 34 LEU cc_start: 0.9230 (tp) cc_final: 0.8957 (tt) REVERT: F 37 LYS cc_start: 0.8587 (ttmt) cc_final: 0.7837 (tptt) REVERT: F 39 SER cc_start: 0.8872 (m) cc_final: 0.8266 (t) REVERT: F 47 TYR cc_start: 0.9036 (t80) cc_final: 0.8665 (t80) REVERT: F 49 SER cc_start: 0.9272 (t) cc_final: 0.8897 (p) REVERT: F 51 LEU cc_start: 0.9231 (tp) cc_final: 0.8974 (tp) REVERT: F 53 GLU cc_start: 0.8471 (tp30) cc_final: 0.7875 (mm-30) REVERT: F 54 TYR cc_start: 0.9047 (t80) cc_final: 0.8642 (t80) REVERT: F 66 LYS cc_start: 0.8653 (tptp) cc_final: 0.7363 (mttm) REVERT: G 11 ASP cc_start: 0.8251 (m-30) cc_final: 0.7954 (t0) REVERT: G 15 LYS cc_start: 0.9092 (ttmt) cc_final: 0.8802 (ttmm) REVERT: G 33 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8860 (mtpp) REVERT: G 37 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7103 (tptt) REVERT: G 69 LYS cc_start: 0.8678 (tttm) cc_final: 0.8365 (tttt) REVERT: H 32 ASP cc_start: 0.7912 (m-30) cc_final: 0.7616 (m-30) REVERT: H 37 LYS cc_start: 0.8135 (ttmt) cc_final: 0.6841 (tptt) REVERT: H 47 TYR cc_start: 0.9174 (t80) cc_final: 0.7417 (t80) REVERT: H 51 LEU cc_start: 0.9334 (tp) cc_final: 0.8709 (tp) REVERT: I 37 LYS cc_start: 0.8769 (ttmt) cc_final: 0.7324 (tptp) REVERT: I 47 TYR cc_start: 0.9058 (t80) cc_final: 0.8817 (t80) REVERT: J 17 ASP cc_start: 0.7627 (m-30) cc_final: 0.7370 (m-30) REVERT: J 22 ASN cc_start: 0.8218 (p0) cc_final: 0.7689 (p0) REVERT: J 24 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7406 (tp-100) REVERT: J 37 LYS cc_start: 0.8886 (ttmt) cc_final: 0.7487 (tptt) REVERT: J 39 SER cc_start: 0.8947 (t) cc_final: 0.8684 (t) REVERT: J 47 TYR cc_start: 0.9239 (t80) cc_final: 0.8421 (t80) REVERT: J 49 SER cc_start: 0.9285 (t) cc_final: 0.8971 (p) REVERT: J 80 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7752 (ttp80) REVERT: K 15 LYS cc_start: 0.9119 (mmtp) cc_final: 0.8851 (tptm) REVERT: K 33 LYS cc_start: 0.9212 (mttt) cc_final: 0.8834 (mtpp) REVERT: K 37 LYS cc_start: 0.9020 (ttmt) cc_final: 0.7592 (tptp) REVERT: K 47 TYR cc_start: 0.9105 (t80) cc_final: 0.7886 (t80) REVERT: L 23 LEU cc_start: 0.8620 (tp) cc_final: 0.8379 (tt) REVERT: L 26 GLN cc_start: 0.8878 (mt0) cc_final: 0.8612 (mt0) REVERT: L 48 GLN cc_start: 0.8830 (tt0) cc_final: 0.8118 (tt0) REVERT: L 53 GLU cc_start: 0.8177 (tp30) cc_final: 0.7838 (tp30) REVERT: L 77 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8147 (tp40) REVERT: M 22 ASN cc_start: 0.8624 (p0) cc_final: 0.8330 (p0) REVERT: M 28 THR cc_start: 0.8814 (m) cc_final: 0.8066 (p) REVERT: M 31 LEU cc_start: 0.9347 (tp) cc_final: 0.9050 (tp) REVERT: M 32 ASP cc_start: 0.8414 (p0) cc_final: 0.8050 (p0) REVERT: M 47 TYR cc_start: 0.9227 (t80) cc_final: 0.8532 (t80) REVERT: M 66 LYS cc_start: 0.8655 (tptt) cc_final: 0.8106 (tmtt) REVERT: N 24 GLN cc_start: 0.8598 (mp10) cc_final: 0.7790 (tm-30) REVERT: N 32 ASP cc_start: 0.8350 (m-30) cc_final: 0.8080 (m-30) REVERT: N 49 SER cc_start: 0.9444 (m) cc_final: 0.9172 (t) REVERT: N 50 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8528 (mmmt) REVERT: N 51 LEU cc_start: 0.9225 (tp) cc_final: 0.8902 (tt) REVERT: N 53 GLU cc_start: 0.8217 (tp30) cc_final: 0.7662 (tp30) REVERT: O 17 ASP cc_start: 0.8210 (m-30) cc_final: 0.7494 (t0) REVERT: O 22 ASN cc_start: 0.9247 (p0) cc_final: 0.7993 (p0) REVERT: O 25 THR cc_start: 0.9060 (m) cc_final: 0.8441 (p) REVERT: O 28 THR cc_start: 0.8423 (m) cc_final: 0.8105 (p) REVERT: O 33 LYS cc_start: 0.9137 (mttt) cc_final: 0.8411 (mtmm) REVERT: O 49 SER cc_start: 0.9214 (m) cc_final: 0.8929 (t) REVERT: O 52 SER cc_start: 0.9064 (m) cc_final: 0.8849 (t) REVERT: O 59 ASN cc_start: 0.8612 (m-40) cc_final: 0.7868 (m110) REVERT: O 69 LYS cc_start: 0.8268 (tttm) cc_final: 0.7723 (ttmt) REVERT: O 77 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8510 (tp-100) REVERT: P 21 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8177 (t0) REVERT: P 22 ASN cc_start: 0.9311 (p0) cc_final: 0.8746 (p0) REVERT: P 29 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: Q 25 THR cc_start: 0.8698 (m) cc_final: 0.8415 (p) REVERT: Q 40 ASP cc_start: 0.8285 (t0) cc_final: 0.7712 (t0) REVERT: Q 49 SER cc_start: 0.9189 (m) cc_final: 0.8763 (t) REVERT: Q 54 TYR cc_start: 0.8611 (t80) cc_final: 0.8349 (t80) REVERT: Q 69 LYS cc_start: 0.8437 (tttm) cc_final: 0.7971 (ttmt) REVERT: R 17 ASP cc_start: 0.7287 (m-30) cc_final: 0.7030 (m-30) REVERT: R 22 ASN cc_start: 0.9112 (p0) cc_final: 0.8714 (p0) REVERT: R 24 GLN cc_start: 0.8216 (mp10) cc_final: 0.7581 (pm20) REVERT: R 33 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8769 (mtpt) REVERT: R 50 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8209 (mmmt) REVERT: R 69 LYS cc_start: 0.8264 (tttm) cc_final: 0.7184 (mttt) REVERT: S 17 ASP cc_start: 0.7766 (m-30) cc_final: 0.7311 (m-30) REVERT: S 33 LYS cc_start: 0.8868 (mttp) cc_final: 0.8293 (mtmt) REVERT: S 39 SER cc_start: 0.9293 (m) cc_final: 0.8388 (m) REVERT: S 58 ARG cc_start: 0.9020 (mmt180) cc_final: 0.8671 (mmt90) REVERT: S 59 ASN cc_start: 0.8563 (m-40) cc_final: 0.7723 (m110) REVERT: T 17 ASP cc_start: 0.8548 (m-30) cc_final: 0.8298 (m-30) REVERT: T 22 ASN cc_start: 0.8843 (p0) cc_final: 0.8502 (p0) REVERT: T 25 THR cc_start: 0.8688 (p) cc_final: 0.8218 (t) REVERT: T 48 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8514 (tm-30) REVERT: T 69 LYS cc_start: 0.6899 (tttm) cc_final: 0.6332 (tttt) outliers start: 61 outliers final: 49 residues processed: 583 average time/residue: 0.2198 time to fit residues: 182.3304 Evaluate side-chains 606 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 553 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 44 LEU 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 G residue 24 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 56 LEU 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 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 27 VAL Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR 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 21 ASP Chi-restraints excluded: chain P residue 29 GLU Chi-restraints excluded: chain P residue 33 LYS 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 67 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 33 LYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN H 77 GLN M 26 GLN M 77 GLN N 48 GLN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.096289 restraints weight = 17826.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099504 restraints weight = 9526.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101662 restraints weight = 6201.613| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4900 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= 0.171 Angle : 0.552 8.427 16112 Z= 0.288 Chirality : 0.040 0.165 1843 Planarity : 0.003 0.020 2109 Dihedral : 3.741 26.659 1596 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.31 % Allowed : 23.76 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1444 helix: 2.02 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -4.09 (0.38), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 5 PHE 0.008 0.001 PHE N 68 TYR 0.025 0.002 TYR E 47 ARG 0.002 0.000 ARG V 58 Details of bonding type rmsd hydrogen bonds : bond 0.03311 ( 893) hydrogen bonds : angle 3.01852 ( 2565) covalent geometry : bond 0.00396 (11837) covalent geometry : angle 0.55187 (16112) *********************** 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 601 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8884 (mmmm) cc_final: 0.8581 (mmmt) REVERT: D 37 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7454 (tptt) REVERT: D 44 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8120 (mt) REVERT: U 15 LYS cc_start: 0.9095 (mttt) cc_final: 0.8846 (mmtp) REVERT: U 22 ASN cc_start: 0.8479 (p0) cc_final: 0.8254 (p0) REVERT: U 37 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7195 (tptt) REVERT: U 66 LYS cc_start: 0.8739 (tptp) cc_final: 0.6656 (mttp) REVERT: V 37 LYS cc_start: 0.8708 (ttmt) cc_final: 0.7619 (tptt) REVERT: V 47 TYR cc_start: 0.9207 (t80) cc_final: 0.8208 (t80) REVERT: V 49 SER cc_start: 0.8599 (t) cc_final: 0.8242 (p) REVERT: V 77 GLN cc_start: 0.8701 (tp40) cc_final: 0.8139 (tp40) REVERT: E 22 ASN cc_start: 0.7998 (p0) cc_final: 0.7315 (p0) REVERT: E 32 ASP cc_start: 0.7854 (m-30) cc_final: 0.7577 (m-30) REVERT: E 37 LYS cc_start: 0.8761 (ttmt) cc_final: 0.7405 (tptt) REVERT: E 53 GLU cc_start: 0.8537 (tp30) cc_final: 0.8100 (mm-30) REVERT: E 66 LYS cc_start: 0.8546 (tptp) cc_final: 0.6969 (mttt) REVERT: F 28 THR cc_start: 0.8722 (m) cc_final: 0.8049 (p) REVERT: F 32 ASP cc_start: 0.7576 (m-30) cc_final: 0.7178 (m-30) REVERT: F 34 LEU cc_start: 0.9217 (tp) cc_final: 0.8942 (tt) REVERT: F 37 LYS cc_start: 0.8617 (ttmt) cc_final: 0.7829 (tptt) REVERT: F 39 SER cc_start: 0.8891 (m) cc_final: 0.8230 (t) REVERT: F 47 TYR cc_start: 0.9057 (t80) cc_final: 0.8533 (t80) REVERT: F 49 SER cc_start: 0.9270 (t) cc_final: 0.8878 (p) REVERT: F 51 LEU cc_start: 0.9210 (tp) cc_final: 0.8924 (tp) REVERT: F 53 GLU cc_start: 0.8232 (tp30) cc_final: 0.7705 (mm-30) REVERT: F 66 LYS cc_start: 0.8635 (tptp) cc_final: 0.7556 (ttmt) REVERT: G 11 ASP cc_start: 0.8254 (m-30) cc_final: 0.7942 (t0) REVERT: G 15 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8780 (ttmm) REVERT: G 37 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7060 (tptt) REVERT: G 66 LYS cc_start: 0.9091 (tppt) cc_final: 0.8660 (tppt) REVERT: G 69 LYS cc_start: 0.8657 (tttm) cc_final: 0.8334 (tttt) REVERT: H 32 ASP cc_start: 0.7831 (m-30) cc_final: 0.7538 (m-30) REVERT: H 37 LYS cc_start: 0.8213 (ttmt) cc_final: 0.6948 (tptt) REVERT: H 47 TYR cc_start: 0.9137 (t80) cc_final: 0.7363 (t80) REVERT: H 51 LEU cc_start: 0.9326 (tp) cc_final: 0.8808 (tp) REVERT: I 37 LYS cc_start: 0.8752 (ttmt) cc_final: 0.7297 (tptp) REVERT: I 47 TYR cc_start: 0.9030 (t80) cc_final: 0.8775 (t80) REVERT: J 17 ASP cc_start: 0.7585 (m-30) cc_final: 0.7342 (m-30) REVERT: J 22 ASN cc_start: 0.8249 (p0) cc_final: 0.7732 (p0) REVERT: J 24 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7510 (tp-100) REVERT: J 31 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (mt) REVERT: J 37 LYS cc_start: 0.8859 (ttmt) cc_final: 0.7471 (tptt) REVERT: J 39 SER cc_start: 0.8918 (t) cc_final: 0.8662 (t) REVERT: J 47 TYR cc_start: 0.9211 (t80) cc_final: 0.8221 (t80) REVERT: J 49 SER cc_start: 0.9254 (t) cc_final: 0.8953 (p) REVERT: K 15 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8731 (tptm) REVERT: K 33 LYS cc_start: 0.9274 (mttt) cc_final: 0.8889 (mtpp) REVERT: K 37 LYS cc_start: 0.9001 (ttmt) cc_final: 0.7553 (tptp) REVERT: K 47 TYR cc_start: 0.9123 (t80) cc_final: 0.7880 (t80) REVERT: K 63 ASN cc_start: 0.8676 (m-40) cc_final: 0.8375 (m110) REVERT: L 26 GLN cc_start: 0.9052 (mt0) cc_final: 0.8775 (tt0) REVERT: L 53 GLU cc_start: 0.8189 (tp30) cc_final: 0.7868 (tp30) REVERT: L 77 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8160 (tp40) REVERT: M 22 ASN cc_start: 0.8672 (p0) cc_final: 0.8330 (p0) REVERT: M 28 THR cc_start: 0.8791 (m) cc_final: 0.8034 (p) REVERT: M 31 LEU cc_start: 0.9319 (tp) cc_final: 0.8982 (tp) REVERT: M 32 ASP cc_start: 0.8387 (p0) cc_final: 0.8055 (p0) REVERT: M 47 TYR cc_start: 0.9171 (t80) cc_final: 0.8626 (t80) REVERT: M 66 LYS cc_start: 0.8614 (tptt) cc_final: 0.8054 (tmtt) REVERT: N 24 GLN cc_start: 0.8579 (mp10) cc_final: 0.7779 (tm-30) REVERT: N 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.8042 (m-30) REVERT: N 49 SER cc_start: 0.9446 (m) cc_final: 0.9151 (t) REVERT: N 50 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8513 (mmmt) REVERT: N 53 GLU cc_start: 0.8189 (tp30) cc_final: 0.7611 (tp30) REVERT: O 15 LYS cc_start: 0.8782 (tppp) cc_final: 0.8465 (tptp) REVERT: O 17 ASP cc_start: 0.8238 (m-30) cc_final: 0.7502 (t0) REVERT: O 22 ASN cc_start: 0.9253 (p0) cc_final: 0.8024 (p0) REVERT: O 25 THR cc_start: 0.9050 (m) cc_final: 0.8421 (p) REVERT: O 28 THR cc_start: 0.8385 (m) cc_final: 0.8076 (p) REVERT: O 33 LYS cc_start: 0.9123 (mttt) cc_final: 0.8389 (mtmm) REVERT: O 47 TYR cc_start: 0.9087 (t80) cc_final: 0.8779 (t80) REVERT: O 49 SER cc_start: 0.9167 (m) cc_final: 0.8899 (t) REVERT: O 52 SER cc_start: 0.8992 (m) cc_final: 0.8743 (t) REVERT: O 59 ASN cc_start: 0.8540 (m-40) cc_final: 0.7814 (m110) REVERT: O 69 LYS cc_start: 0.8230 (tttm) cc_final: 0.7680 (ttmt) REVERT: O 77 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8558 (tp-100) REVERT: P 22 ASN cc_start: 0.9339 (p0) cc_final: 0.8748 (p0) REVERT: P 29 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: P 33 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8871 (ttmt) REVERT: Q 25 THR cc_start: 0.8668 (m) cc_final: 0.8401 (p) REVERT: Q 40 ASP cc_start: 0.8222 (t0) cc_final: 0.7651 (t0) REVERT: Q 49 SER cc_start: 0.9182 (m) cc_final: 0.8699 (t) REVERT: Q 54 TYR cc_start: 0.8614 (t80) cc_final: 0.8285 (t80) REVERT: Q 69 LYS cc_start: 0.8419 (tttm) cc_final: 0.7942 (ttmt) REVERT: R 22 ASN cc_start: 0.9179 (p0) cc_final: 0.8774 (p0) REVERT: R 24 GLN cc_start: 0.8208 (mp10) cc_final: 0.7829 (pm20) REVERT: R 69 LYS cc_start: 0.8234 (tttm) cc_final: 0.6917 (mttt) REVERT: S 17 ASP cc_start: 0.7722 (m-30) cc_final: 0.7307 (m-30) REVERT: S 39 SER cc_start: 0.9312 (m) cc_final: 0.8378 (m) REVERT: S 59 ASN cc_start: 0.8531 (m-40) cc_final: 0.7396 (m110) REVERT: T 17 ASP cc_start: 0.8046 (m-30) cc_final: 0.7817 (m-30) REVERT: T 22 ASN cc_start: 0.8892 (p0) cc_final: 0.8538 (p0) REVERT: T 25 THR cc_start: 0.8657 (p) cc_final: 0.8190 (t) REVERT: T 48 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8522 (tm-30) REVERT: T 50 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8629 (mmmt) REVERT: T 69 LYS cc_start: 0.6930 (tttm) cc_final: 0.6344 (tttt) outliers start: 54 outliers final: 48 residues processed: 565 average time/residue: 0.2192 time to fit residues: 177.2135 Evaluate side-chains 588 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 536 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 44 LEU 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 F residue 24 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 31 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 M residue 69 LYS Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 64 THR 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 33 LYS 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 12 VAL Chi-restraints excluded: chain R residue 13 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN D 77 GLN H 77 GLN K 55 ASN L 48 GLN M 77 GLN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.095650 restraints weight = 17757.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098816 restraints weight = 9376.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100908 restraints weight = 6060.273| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11837 Z= 0.167 Angle : 0.564 8.748 16112 Z= 0.292 Chirality : 0.040 0.163 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.747 26.877 1596 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.15 % Allowed : 24.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.22), residues: 1444 helix: 2.03 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -3.94 (0.39), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 5 PHE 0.009 0.001 PHE O 16 TYR 0.030 0.002 TYR E 47 ARG 0.002 0.000 ARG V 58 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 893) hydrogen bonds : angle 3.02773 ( 2565) covalent geometry : bond 0.00390 (11837) covalent geometry : angle 0.56443 (16112) *********************** 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 603 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 551 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8681 (mmmt) REVERT: D 37 LYS cc_start: 0.8599 (ttmt) cc_final: 0.7601 (tptt) REVERT: U 15 LYS cc_start: 0.9092 (mttt) cc_final: 0.8842 (mmtp) REVERT: U 22 ASN cc_start: 0.8415 (p0) cc_final: 0.8155 (p0) REVERT: U 37 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7203 (tptt) REVERT: U 66 LYS cc_start: 0.8733 (tptp) cc_final: 0.6644 (mttp) REVERT: U 77 GLN cc_start: 0.8873 (tp40) cc_final: 0.8635 (tp40) REVERT: V 37 LYS cc_start: 0.8757 (ttmt) cc_final: 0.7556 (tptt) REVERT: V 47 TYR cc_start: 0.9184 (t80) cc_final: 0.8034 (t80) REVERT: V 49 SER cc_start: 0.8593 (t) cc_final: 0.8242 (p) REVERT: V 77 GLN cc_start: 0.8709 (tp40) cc_final: 0.7872 (tp-100) REVERT: E 21 ASP cc_start: 0.7645 (m-30) cc_final: 0.7347 (m-30) REVERT: E 22 ASN cc_start: 0.7973 (p0) cc_final: 0.7279 (p0) REVERT: E 32 ASP cc_start: 0.7848 (m-30) cc_final: 0.7561 (m-30) REVERT: E 37 LYS cc_start: 0.8784 (ttmt) cc_final: 0.7570 (tptt) REVERT: E 53 GLU cc_start: 0.8544 (tp30) cc_final: 0.8110 (mm-30) REVERT: E 66 LYS cc_start: 0.8607 (tptp) cc_final: 0.6976 (mttt) REVERT: F 28 THR cc_start: 0.8730 (m) cc_final: 0.8517 (p) REVERT: F 34 LEU cc_start: 0.9203 (tp) cc_final: 0.8938 (tt) REVERT: F 37 LYS cc_start: 0.8636 (ttmt) cc_final: 0.7829 (tptt) REVERT: F 39 SER cc_start: 0.8872 (m) cc_final: 0.8261 (t) REVERT: F 47 TYR cc_start: 0.9050 (t80) cc_final: 0.8545 (t80) REVERT: F 49 SER cc_start: 0.9271 (t) cc_final: 0.8860 (p) REVERT: F 51 LEU cc_start: 0.9207 (tp) cc_final: 0.8924 (tp) REVERT: F 53 GLU cc_start: 0.8346 (tp30) cc_final: 0.7898 (mm-30) REVERT: F 63 ASN cc_start: 0.9152 (m-40) cc_final: 0.8934 (m110) REVERT: F 66 LYS cc_start: 0.8621 (tptp) cc_final: 0.7556 (ttmt) REVERT: G 11 ASP cc_start: 0.8168 (m-30) cc_final: 0.7901 (t0) REVERT: G 15 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8767 (ttmm) REVERT: G 37 LYS cc_start: 0.8387 (ttmt) cc_final: 0.7045 (tptt) REVERT: G 66 LYS cc_start: 0.9024 (tppt) cc_final: 0.8443 (tppt) REVERT: G 69 LYS cc_start: 0.8648 (tttm) cc_final: 0.8293 (tttt) REVERT: H 32 ASP cc_start: 0.7848 (m-30) cc_final: 0.7542 (m-30) REVERT: H 37 LYS cc_start: 0.8504 (ttmt) cc_final: 0.7196 (tptt) REVERT: H 47 TYR cc_start: 0.9137 (t80) cc_final: 0.7368 (t80) REVERT: H 51 LEU cc_start: 0.9328 (tp) cc_final: 0.8796 (tp) REVERT: I 37 LYS cc_start: 0.8712 (ttmt) cc_final: 0.7217 (tptp) REVERT: J 17 ASP cc_start: 0.7596 (m-30) cc_final: 0.7336 (m-30) REVERT: J 21 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7682 (t0) REVERT: J 22 ASN cc_start: 0.8292 (p0) cc_final: 0.7743 (p0) REVERT: J 24 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7551 (tp-100) REVERT: J 37 LYS cc_start: 0.8831 (ttmt) cc_final: 0.7440 (tptt) REVERT: J 39 SER cc_start: 0.8934 (t) cc_final: 0.8675 (t) REVERT: J 49 SER cc_start: 0.9244 (t) cc_final: 0.8942 (p) REVERT: K 15 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8701 (tptm) REVERT: K 33 LYS cc_start: 0.9274 (mttt) cc_final: 0.8885 (mtpp) REVERT: K 37 LYS cc_start: 0.8986 (ttmt) cc_final: 0.7544 (tptp) REVERT: K 47 TYR cc_start: 0.9110 (t80) cc_final: 0.7858 (t80) REVERT: K 63 ASN cc_start: 0.8667 (m-40) cc_final: 0.8339 (m110) REVERT: L 26 GLN cc_start: 0.9047 (mt0) cc_final: 0.8782 (tt0) REVERT: L 53 GLU cc_start: 0.8203 (tp30) cc_final: 0.7843 (tp30) REVERT: L 77 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8189 (tp40) REVERT: M 22 ASN cc_start: 0.8663 (p0) cc_final: 0.8327 (p0) REVERT: M 28 THR cc_start: 0.8769 (m) cc_final: 0.7993 (p) REVERT: M 31 LEU cc_start: 0.9324 (tp) cc_final: 0.8995 (tp) REVERT: M 32 ASP cc_start: 0.8388 (p0) cc_final: 0.8043 (p0) REVERT: M 47 TYR cc_start: 0.9176 (t80) cc_final: 0.8566 (t80) REVERT: M 66 LYS cc_start: 0.8584 (tptt) cc_final: 0.8038 (tmtt) REVERT: N 24 GLN cc_start: 0.8552 (mp10) cc_final: 0.7785 (tm-30) REVERT: N 32 ASP cc_start: 0.8310 (m-30) cc_final: 0.8076 (m-30) REVERT: N 49 SER cc_start: 0.9434 (m) cc_final: 0.9105 (t) REVERT: N 51 LEU cc_start: 0.9151 (tp) cc_final: 0.8899 (tt) REVERT: N 53 GLU cc_start: 0.8199 (tp30) cc_final: 0.7601 (tp30) REVERT: O 15 LYS cc_start: 0.8785 (tppp) cc_final: 0.8474 (tptp) REVERT: O 17 ASP cc_start: 0.8249 (m-30) cc_final: 0.7499 (t0) REVERT: O 22 ASN cc_start: 0.9239 (p0) cc_final: 0.8007 (p0) REVERT: O 25 THR cc_start: 0.9056 (m) cc_final: 0.8419 (p) REVERT: O 28 THR cc_start: 0.8380 (m) cc_final: 0.8069 (p) REVERT: O 33 LYS cc_start: 0.9100 (mttt) cc_final: 0.8367 (mtmm) REVERT: O 47 TYR cc_start: 0.9094 (t80) cc_final: 0.8752 (t80) REVERT: O 49 SER cc_start: 0.9187 (m) cc_final: 0.8912 (t) REVERT: O 59 ASN cc_start: 0.8558 (m-40) cc_final: 0.7856 (m110) REVERT: O 69 LYS cc_start: 0.8116 (tttm) cc_final: 0.7529 (ttmt) REVERT: O 77 GLN cc_start: 0.8911 (tp-100) cc_final: 0.8579 (tp-100) REVERT: P 22 ASN cc_start: 0.9325 (p0) cc_final: 0.8770 (p0) REVERT: P 29 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: P 33 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8934 (ttmt) REVERT: P 49 SER cc_start: 0.9277 (m) cc_final: 0.9061 (p) REVERT: Q 25 THR cc_start: 0.8718 (m) cc_final: 0.8445 (p) REVERT: Q 40 ASP cc_start: 0.8233 (t0) cc_final: 0.7653 (t0) REVERT: Q 54 TYR cc_start: 0.8622 (t80) cc_final: 0.8056 (t80) REVERT: Q 69 LYS cc_start: 0.8412 (tttm) cc_final: 0.7950 (ttmt) REVERT: R 22 ASN cc_start: 0.9144 (p0) cc_final: 0.8903 (p0) REVERT: R 24 GLN cc_start: 0.8199 (mp10) cc_final: 0.7511 (pm20) REVERT: R 59 ASN cc_start: 0.8424 (m-40) cc_final: 0.7428 (m110) REVERT: R 69 LYS cc_start: 0.8232 (tttm) cc_final: 0.7317 (ttmt) REVERT: S 17 ASP cc_start: 0.7776 (m-30) cc_final: 0.7329 (m-30) REVERT: S 33 LYS cc_start: 0.8895 (mttp) cc_final: 0.8461 (mtmt) REVERT: S 39 SER cc_start: 0.9303 (m) cc_final: 0.8382 (m) REVERT: S 58 ARG cc_start: 0.9023 (mmt180) cc_final: 0.8693 (mmt90) REVERT: S 59 ASN cc_start: 0.8518 (m-40) cc_final: 0.7368 (m110) REVERT: T 17 ASP cc_start: 0.8075 (m-30) cc_final: 0.7837 (m-30) REVERT: T 22 ASN cc_start: 0.8859 (p0) cc_final: 0.8487 (p0) REVERT: T 25 THR cc_start: 0.8667 (p) cc_final: 0.8195 (t) REVERT: T 48 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8526 (tm-30) REVERT: T 50 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8608 (mmmt) REVERT: T 69 LYS cc_start: 0.6945 (tttm) cc_final: 0.6358 (tttt) outliers start: 52 outliers final: 46 residues processed: 568 average time/residue: 0.2293 time to fit residues: 186.8818 Evaluate side-chains 589 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 540 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 H residue 28 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 21 ASP 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 69 LYS Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR 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 33 LYS 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 13 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN M 77 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.097224 restraints weight = 17724.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100432 restraints weight = 9429.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102616 restraints weight = 6125.265| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11837 Z= 0.161 Angle : 0.562 8.341 16112 Z= 0.293 Chirality : 0.040 0.155 1843 Planarity : 0.003 0.019 2109 Dihedral : 3.740 26.337 1596 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.75 % Allowed : 25.60 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.22), residues: 1444 helix: 2.08 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -3.89 (0.40), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 5 PHE 0.008 0.001 PHE O 16 TYR 0.030 0.002 TYR E 47 ARG 0.002 0.000 ARG V 58 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 893) hydrogen bonds : angle 3.02598 ( 2565) covalent geometry : bond 0.00377 (11837) covalent geometry : angle 0.56185 (16112) ********************** 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 595 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 548 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: D 15 LYS cc_start: 0.8908 (mmmm) cc_final: 0.8689 (mmmt) REVERT: D 37 LYS cc_start: 0.8699 (ttmt) cc_final: 0.7696 (tptt) REVERT: U 15 LYS cc_start: 0.9102 (mttt) cc_final: 0.8866 (mmtp) REVERT: U 22 ASN cc_start: 0.8515 (p0) cc_final: 0.8263 (p0) REVERT: U 37 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7230 (tptt) REVERT: U 66 LYS cc_start: 0.8751 (tptp) cc_final: 0.6700 (mttp) REVERT: U 77 GLN cc_start: 0.8778 (tp40) cc_final: 0.8521 (tp40) REVERT: V 37 LYS cc_start: 0.8687 (ttmt) cc_final: 0.7574 (tptt) REVERT: V 47 TYR cc_start: 0.9179 (t80) cc_final: 0.8057 (t80) REVERT: V 49 SER cc_start: 0.8660 (t) cc_final: 0.8329 (p) REVERT: V 77 GLN cc_start: 0.8738 (tp40) cc_final: 0.7921 (tp-100) REVERT: E 21 ASP cc_start: 0.7545 (m-30) cc_final: 0.7241 (m-30) REVERT: E 22 ASN cc_start: 0.8214 (p0) cc_final: 0.7591 (p0) REVERT: E 37 LYS cc_start: 0.8804 (ttmt) cc_final: 0.7601 (tptt) REVERT: E 66 LYS cc_start: 0.8663 (tptp) cc_final: 0.7052 (mttt) REVERT: F 34 LEU cc_start: 0.9234 (tp) cc_final: 0.8967 (tt) REVERT: F 37 LYS cc_start: 0.8669 (ttmt) cc_final: 0.7706 (tptt) REVERT: F 39 SER cc_start: 0.8879 (m) cc_final: 0.8244 (t) REVERT: F 47 TYR cc_start: 0.9026 (t80) cc_final: 0.8540 (t80) REVERT: F 49 SER cc_start: 0.9251 (t) cc_final: 0.8855 (p) REVERT: F 51 LEU cc_start: 0.9224 (tp) cc_final: 0.8956 (tp) REVERT: F 53 GLU cc_start: 0.8297 (tp30) cc_final: 0.7832 (mm-30) REVERT: F 63 ASN cc_start: 0.9150 (m-40) cc_final: 0.8942 (m110) REVERT: F 66 LYS cc_start: 0.8626 (tptp) cc_final: 0.7568 (ttmt) REVERT: G 11 ASP cc_start: 0.8156 (m-30) cc_final: 0.7906 (t0) REVERT: G 15 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8901 (ttmm) REVERT: G 37 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7037 (tptt) REVERT: G 66 LYS cc_start: 0.9033 (tppt) cc_final: 0.8526 (tppt) REVERT: G 69 LYS cc_start: 0.8669 (tttm) cc_final: 0.8331 (tttt) REVERT: H 32 ASP cc_start: 0.7690 (m-30) cc_final: 0.7430 (m-30) REVERT: H 37 LYS cc_start: 0.8658 (ttmt) cc_final: 0.7254 (tptt) REVERT: H 47 TYR cc_start: 0.9128 (t80) cc_final: 0.7384 (t80) REVERT: H 51 LEU cc_start: 0.9349 (tp) cc_final: 0.8820 (tp) REVERT: H 54 TYR cc_start: 0.9049 (t80) cc_final: 0.8541 (t80) REVERT: I 37 LYS cc_start: 0.8706 (ttmt) cc_final: 0.7195 (tptp) REVERT: J 17 ASP cc_start: 0.7507 (m-30) cc_final: 0.7280 (m-30) REVERT: J 22 ASN cc_start: 0.8249 (p0) cc_final: 0.7723 (p0) REVERT: J 24 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7481 (tp-100) REVERT: J 37 LYS cc_start: 0.8794 (ttmt) cc_final: 0.7438 (tptt) REVERT: J 39 SER cc_start: 0.8886 (t) cc_final: 0.8610 (t) REVERT: J 47 TYR cc_start: 0.9055 (t80) cc_final: 0.8207 (t80) REVERT: J 49 SER cc_start: 0.9225 (t) cc_final: 0.8997 (p) REVERT: J 51 LEU cc_start: 0.9297 (tp) cc_final: 0.8905 (tp) REVERT: K 33 LYS cc_start: 0.9284 (mttt) cc_final: 0.8893 (mtpp) REVERT: K 37 LYS cc_start: 0.8985 (ttmt) cc_final: 0.7689 (tptp) REVERT: K 47 TYR cc_start: 0.9107 (t80) cc_final: 0.7860 (t80) REVERT: K 63 ASN cc_start: 0.8684 (m-40) cc_final: 0.8358 (m110) REVERT: L 26 GLN cc_start: 0.9056 (mt0) cc_final: 0.8767 (tt0) REVERT: L 53 GLU cc_start: 0.8184 (tp30) cc_final: 0.7847 (tp30) REVERT: L 77 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8436 (tp40) REVERT: M 22 ASN cc_start: 0.8693 (p0) cc_final: 0.8370 (p0) REVERT: M 28 THR cc_start: 0.8778 (m) cc_final: 0.8004 (p) REVERT: M 31 LEU cc_start: 0.9336 (tp) cc_final: 0.9005 (tp) REVERT: M 32 ASP cc_start: 0.8386 (p0) cc_final: 0.8035 (p0) REVERT: M 47 TYR cc_start: 0.9177 (t80) cc_final: 0.8590 (t80) REVERT: M 66 LYS cc_start: 0.8619 (tptt) cc_final: 0.8080 (tmtt) REVERT: N 24 GLN cc_start: 0.8517 (mp10) cc_final: 0.7798 (tm-30) REVERT: N 32 ASP cc_start: 0.8276 (m-30) cc_final: 0.8049 (m-30) REVERT: N 49 SER cc_start: 0.9441 (m) cc_final: 0.9126 (t) REVERT: N 51 LEU cc_start: 0.9181 (tp) cc_final: 0.8907 (tt) REVERT: N 53 GLU cc_start: 0.8165 (tp30) cc_final: 0.7854 (tp30) REVERT: O 15 LYS cc_start: 0.8800 (tppp) cc_final: 0.8473 (tptp) REVERT: O 17 ASP cc_start: 0.8217 (m-30) cc_final: 0.7485 (t0) REVERT: O 22 ASN cc_start: 0.9228 (p0) cc_final: 0.8078 (p0) REVERT: O 25 THR cc_start: 0.9039 (m) cc_final: 0.8426 (p) REVERT: O 28 THR cc_start: 0.8413 (m) cc_final: 0.8088 (p) REVERT: O 33 LYS cc_start: 0.9101 (mttt) cc_final: 0.8393 (mtmm) REVERT: O 49 SER cc_start: 0.9210 (m) cc_final: 0.8725 (t) REVERT: O 59 ASN cc_start: 0.8556 (m-40) cc_final: 0.7889 (m110) REVERT: O 69 LYS cc_start: 0.8107 (tttm) cc_final: 0.7542 (ttmt) REVERT: O 77 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8576 (tp-100) REVERT: P 22 ASN cc_start: 0.9315 (p0) cc_final: 0.8699 (p0) REVERT: P 29 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: P 33 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9015 (ttmt) REVERT: P 49 SER cc_start: 0.9287 (m) cc_final: 0.9086 (p) REVERT: Q 25 THR cc_start: 0.8836 (m) cc_final: 0.8519 (p) REVERT: Q 40 ASP cc_start: 0.8211 (t0) cc_final: 0.7651 (t0) REVERT: Q 49 SER cc_start: 0.9215 (m) cc_final: 0.8682 (t) REVERT: Q 54 TYR cc_start: 0.8640 (t80) cc_final: 0.8089 (t80) REVERT: Q 69 LYS cc_start: 0.8425 (tttm) cc_final: 0.7939 (ttmt) REVERT: R 22 ASN cc_start: 0.9145 (p0) cc_final: 0.8881 (p0) REVERT: R 24 GLN cc_start: 0.8183 (mp10) cc_final: 0.7796 (pm20) REVERT: R 59 ASN cc_start: 0.8405 (m-40) cc_final: 0.7417 (m110) REVERT: R 69 LYS cc_start: 0.8254 (tttm) cc_final: 0.7328 (ttmt) REVERT: S 17 ASP cc_start: 0.7801 (m-30) cc_final: 0.7350 (m-30) REVERT: S 33 LYS cc_start: 0.8911 (mttp) cc_final: 0.8550 (mtmt) REVERT: S 39 SER cc_start: 0.9309 (m) cc_final: 0.8663 (p) REVERT: S 58 ARG cc_start: 0.9043 (mmt180) cc_final: 0.8690 (mmt90) REVERT: S 59 ASN cc_start: 0.8483 (m-40) cc_final: 0.7351 (m110) REVERT: T 17 ASP cc_start: 0.8049 (m-30) cc_final: 0.7828 (m-30) REVERT: T 22 ASN cc_start: 0.8880 (p0) cc_final: 0.8513 (p0) REVERT: T 25 THR cc_start: 0.8592 (p) cc_final: 0.8141 (t) REVERT: T 48 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8520 (tm-30) REVERT: T 69 LYS cc_start: 0.6985 (tttm) cc_final: 0.6416 (tttt) outliers start: 47 outliers final: 44 residues processed: 566 average time/residue: 0.2181 time to fit residues: 175.9090 Evaluate side-chains 584 residues out of total 1254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 538 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 56 LEU 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 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 69 LYS Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 34 LEU Chi-restraints excluded: chain N residue 64 THR 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 33 LYS 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 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 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 64 THR 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 84 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 115 optimal weight: 0.0370 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN H 77 GLN M 77 GLN S 26 GLN ** S 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097301 restraints weight = 17728.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.100524 restraints weight = 9411.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102670 restraints weight = 6091.955| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11837 Z= 0.150 Angle : 0.563 8.082 16112 Z= 0.292 Chirality : 0.039 0.153 1843 Planarity : 0.003 0.022 2109 Dihedral : 3.713 25.676 1596 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.51 % Allowed : 26.40 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.22), residues: 1444 helix: 2.20 (0.14), residues: 1273 sheet: None (None), residues: 0 loop : -2.68 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 5 PHE 0.008 0.001 PHE O 16 TYR 0.030 0.002 TYR E 47 ARG 0.002 0.000 ARG V 58 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 893) hydrogen bonds : angle 3.01934 ( 2565) covalent geometry : bond 0.00351 (11837) covalent geometry : angle 0.56341 (16112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.20 seconds wall clock time: 73 minutes 49.00 seconds (4429.00 seconds total)