Starting phenix.real_space_refine on Thu Mar 5 05:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vk9_21225/03_2026/6vk9_21225.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 12432 2.51 5 N 3232 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "D" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 773 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 101} Restraints were copied for chains: O, Q, S, U, G, I, K, M, C, E, W, Y, 0, 2, 4, B, P, R, T, V, H, J, L, N, F, X, Z, 1, 3, 5 Time building chain proxies: 1.30, per 1000 atoms: 0.07 Number of scatterers: 19808 At special positions: 0 Unit cell: (81.378, 81.378, 255.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 4128 8.00 N 3232 7.00 C 12432 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 889.9 milliseconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 16 sheets defined 25.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL O 10 " --> pdb=" O LEU O 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 11 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA O 31 " --> pdb=" O TYR O 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER O 38 " --> pdb=" O SER O 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA O 52 " --> pdb=" O GLU O 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL Q 10 " --> pdb=" O LEU Q 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Q 11 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Q 14 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 55 removed outlier: 4.783A pdb=" N ALA Q 31 " --> pdb=" O TYR Q 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Q 38 " --> pdb=" O SER Q 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR Q 45 " --> pdb=" O ARG Q 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA Q 52 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL S 10 " --> pdb=" O LEU S 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA S 31 " --> pdb=" O TYR S 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA S 52 " --> pdb=" O GLU S 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL U 10 " --> pdb=" O LEU U 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA U 11 " --> pdb=" O LEU U 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY U 14 " --> pdb=" O VAL U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA U 31 " --> pdb=" O TYR U 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER U 38 " --> pdb=" O SER U 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR U 45 " --> pdb=" O ARG U 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA U 52 " --> pdb=" O GLU U 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL G 10 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR G 45 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL I 10 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA I 31 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL K 10 " --> pdb=" O LEU K 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY K 14 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA K 31 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 38 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA K 52 " --> pdb=" O GLU K 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL M 10 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY M 14 " --> pdb=" O VAL M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA M 31 " --> pdb=" O TYR M 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR M 45 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA M 52 " --> pdb=" O GLU M 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL C 10 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 14 " --> pdb=" O VAL E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 55 removed outlier: 4.781A pdb=" N ALA E 31 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E 52 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL W 10 " --> pdb=" O LEU W 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY W 14 " --> pdb=" O VAL W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA W 31 " --> pdb=" O TYR W 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER W 38 " --> pdb=" O SER W 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR W 45 " --> pdb=" O ARG W 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA W 52 " --> pdb=" O GLU W 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 14 removed outlier: 4.276A pdb=" N VAL Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Y 11 " --> pdb=" O LEU Y 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY Y 14 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA Y 31 " --> pdb=" O TYR Y 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER Y 38 " --> pdb=" O SER Y 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) Processing helix chain '0' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 0 10 " --> pdb=" O LEU 0 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 0 11 " --> pdb=" O LEU 0 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 0 14 " --> pdb=" O VAL 0 10 " (cutoff:3.500A) Processing helix chain '0' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 0 31 " --> pdb=" O TYR 0 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 0 38 " --> pdb=" O SER 0 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 0 45 " --> pdb=" O ARG 0 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 0 52 " --> pdb=" O GLU 0 48 " (cutoff:3.500A) Processing helix chain '2' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 2 10 " --> pdb=" O LEU 2 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 2 11 " --> pdb=" O LEU 2 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 2 14 " --> pdb=" O VAL 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 2 31 " --> pdb=" O TYR 2 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 2 38 " --> pdb=" O SER 2 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 2 52 " --> pdb=" O GLU 2 48 " (cutoff:3.500A) Processing helix chain '4' and resid 4 through 14 removed outlier: 4.277A pdb=" N VAL 4 10 " --> pdb=" O LEU 4 6 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA 4 11 " --> pdb=" O LEU 4 7 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY 4 14 " --> pdb=" O VAL 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 55 removed outlier: 4.782A pdb=" N ALA 4 31 " --> pdb=" O TYR 4 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 4 38 " --> pdb=" O SER 4 34 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR 4 45 " --> pdb=" O ARG 4 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 4 52 " --> pdb=" O GLU 4 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 22 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 28 Processing sheet with id=AA3, first strand: chain 'P' and resid 22 through 28 Processing sheet with id=AA4, first strand: chain 'R' and resid 22 through 28 Processing sheet with id=AA5, first strand: chain 'T' and resid 22 through 28 Processing sheet with id=AA6, first strand: chain 'V' and resid 22 through 28 Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 28 Processing sheet with id=AA8, first strand: chain 'J' and resid 22 through 28 Processing sheet with id=AA9, first strand: chain 'L' and resid 22 through 28 Processing sheet with id=AB1, first strand: chain 'N' and resid 22 through 28 Processing sheet with id=AB2, first strand: chain 'F' and resid 22 through 28 Processing sheet with id=AB3, first strand: chain 'X' and resid 22 through 28 Processing sheet with id=AB4, first strand: chain 'Z' and resid 22 through 28 Processing sheet with id=AB5, first strand: chain '1' and resid 22 through 28 Processing sheet with id=AB6, first strand: chain '3' and resid 22 through 28 Processing sheet with id=AB7, first strand: chain '5' and resid 22 through 28 624 hydrogen bonds defined for protein. 1824 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: 2.77 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4197 1.33 - 1.45: 4847 1.45 - 1.57: 11100 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 20176 Sorted by residual: bond pdb=" CA PRO C 58 " pdb=" C PRO C 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.24e+01 bond pdb=" CA PRO 2 58 " pdb=" C PRO 2 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" CA PRO S 58 " pdb=" C PRO S 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.18e+01 bond pdb=" CA PRO K 58 " pdb=" C PRO K 58 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.16e+01 bond pdb=" CA PRO G 58 " pdb=" C PRO G 58 " ideal model delta sigma weight residual 1.514 1.540 -0.025 5.50e-03 3.31e+04 2.15e+01 ... (remaining 20171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 20531 1.60 - 3.19: 5152 3.19 - 4.78: 1582 4.78 - 6.38: 223 6.38 - 7.97: 16 Bond angle restraints: 27504 Sorted by residual: angle pdb=" N THR P 15 " pdb=" CA THR P 15 " pdb=" C THR P 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.44e+01 angle pdb=" N THR X 15 " pdb=" CA THR X 15 " pdb=" C THR X 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.44e+01 angle pdb=" N THR 5 15 " pdb=" CA THR 5 15 " pdb=" C THR 5 15 " ideal model delta sigma weight residual 111.30 119.27 -7.97 1.36e+00 5.41e-01 3.43e+01 angle pdb=" N THR Z 15 " pdb=" CA THR Z 15 " pdb=" C THR Z 15 " ideal model delta sigma weight residual 111.30 119.26 -7.96 1.36e+00 5.41e-01 3.43e+01 angle pdb=" N THR J 15 " pdb=" CA THR J 15 " pdb=" C THR J 15 " ideal model delta sigma weight residual 111.30 119.25 -7.95 1.36e+00 5.41e-01 3.42e+01 ... (remaining 27499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10768 16.93 - 33.85: 768 33.85 - 50.77: 208 50.77 - 67.70: 64 67.70 - 84.62: 16 Dihedral angle restraints: 11824 sinusoidal: 4224 harmonic: 7600 Sorted by residual: dihedral pdb=" CA THR N 62 " pdb=" C THR N 62 " pdb=" N SER N 63 " pdb=" CA SER N 63 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR T 62 " pdb=" C THR T 62 " pdb=" N SER T 63 " pdb=" CA SER T 63 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA THR X 62 " pdb=" C THR X 62 " pdb=" N SER X 63 " pdb=" CA SER X 63 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 11821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2427 0.085 - 0.169: 573 0.169 - 0.254: 216 0.254 - 0.339: 16 0.339 - 0.424: 16 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA THR X 15 " pdb=" N THR X 15 " pdb=" C THR X 15 " pdb=" CB THR X 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA THR R 15 " pdb=" N THR R 15 " pdb=" C THR R 15 " pdb=" CB THR R 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA THR J 15 " pdb=" N THR J 15 " pdb=" C THR J 15 " pdb=" CB THR J 15 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3245 not shown) Planarity restraints: 3520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 43 " 0.071 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR 1 43 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 43 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 43 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 43 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 43 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR 1 43 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR 1 43 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 43 " -0.071 2.00e-02 2.50e+03 4.41e-02 3.89e+01 pdb=" CG TYR N 43 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR N 43 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR N 43 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR N 43 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR N 43 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR N 43 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR N 43 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 3 43 " -0.071 2.00e-02 2.50e+03 4.41e-02 3.88e+01 pdb=" CG TYR 3 43 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR 3 43 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 3 43 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR 3 43 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR 3 43 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR 3 43 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR 3 43 " -0.077 2.00e-02 2.50e+03 ... (remaining 3517 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 106 2.60 - 3.17: 19613 3.17 - 3.75: 29996 3.75 - 4.32: 43928 4.32 - 4.90: 69370 Nonbonded interactions: 163013 Sorted by model distance: nonbonded pdb=" NZ LYS S 30 " pdb=" OD1 ASP M 53 " model vdw 2.023 3.120 nonbonded pdb=" NZ LYS K 30 " pdb=" OD1 ASP E 53 " model vdw 2.043 3.120 nonbonded pdb=" OD1 ASP W 53 " pdb=" NZ LYS 2 30 " model vdw 2.085 3.120 nonbonded pdb=" NZ LYS I 30 " pdb=" OD1 ASP C 53 " model vdw 2.088 3.120 nonbonded pdb=" NZ LYS Q 30 " pdb=" OD1 ASP K 53 " model vdw 2.090 3.120 ... (remaining 163008 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'C' selection = chain 'E' selection = chain 'W' selection = chain 'Y' selection = chain '0' selection = chain '2' selection = chain '4' } ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'F' selection = chain 'X' selection = chain 'Z' selection = chain '1' selection = chain '3' selection = chain '5' } 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: 4.850 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.010 0.049 20176 Z= 0.648 Angle : 1.574 7.975 27504 Z= 1.023 Chirality : 0.090 0.424 3248 Planarity : 0.012 0.068 3520 Dihedral : 13.960 84.624 6928 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.14), residues: 2576 helix: -3.46 (0.12), residues: 752 sheet: 0.08 (0.19), residues: 320 loop : -2.95 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 28 TYR 0.077 0.018 TYR N 43 PHE 0.065 0.009 PHE O 51 TRP 0.071 0.012 TRP V 66 Details of bonding type rmsd covalent geometry : bond 0.01050 (20176) covalent geometry : angle 1.57367 (27504) hydrogen bonds : bond 0.21388 ( 624) hydrogen bonds : angle 8.16483 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 945 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASN cc_start: 0.8925 (t0) cc_final: 0.8416 (m-40) REVERT: A 51 PHE cc_start: 0.8622 (t80) cc_final: 0.8089 (t80) REVERT: Q 23 GLN cc_start: 0.7779 (mp10) cc_final: 0.7515 (mp10) REVERT: G 23 GLN cc_start: 0.8371 (mp10) cc_final: 0.8020 (mp10) REVERT: G 28 ARG cc_start: 0.8662 (ttp-170) cc_final: 0.8428 (ttm110) REVERT: G 42 ASN cc_start: 0.8652 (t0) cc_final: 0.8422 (t0) REVERT: I 42 ASN cc_start: 0.8415 (t0) cc_final: 0.8083 (m-40) REVERT: C 42 ASN cc_start: 0.8779 (t0) cc_final: 0.8419 (t0) REVERT: C 51 PHE cc_start: 0.8841 (t80) cc_final: 0.8095 (t80) REVERT: C 58 PRO cc_start: 0.9242 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: E 23 GLN cc_start: 0.8494 (mp10) cc_final: 0.8246 (pm20) REVERT: E 41 ARG cc_start: 0.8888 (tmt-80) cc_final: 0.8552 (tmt170) REVERT: E 42 ASN cc_start: 0.8713 (t0) cc_final: 0.8258 (t0) REVERT: E 51 PHE cc_start: 0.8913 (t80) cc_final: 0.8209 (t80) REVERT: E 58 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.9130 (Cg_endo) REVERT: Y 41 ARG cc_start: 0.8478 (tmt-80) cc_final: 0.7655 (ttp-170) REVERT: Y 55 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8704 (mp10) REVERT: Y 60 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7099 (tm-30) REVERT: 0 41 ARG cc_start: 0.8664 (tmt-80) cc_final: 0.7521 (ttp-170) REVERT: 4 37 SER cc_start: 0.9287 (p) cc_final: 0.8892 (p) REVERT: 4 41 ARG cc_start: 0.8849 (tmt-80) cc_final: 0.7776 (ttp-170) REVERT: D 21 ASN cc_start: 0.8864 (t0) cc_final: 0.8650 (t0) REVERT: D 56 PHE cc_start: 0.9071 (m-80) cc_final: 0.8712 (m-10) REVERT: D 76 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7783 (mmmm) REVERT: B 17 LYS cc_start: 0.9011 (mmtt) cc_final: 0.8596 (mmmt) REVERT: B 21 ASN cc_start: 0.8766 (t0) cc_final: 0.8461 (t0) REVERT: B 49 ASN cc_start: 0.9098 (t0) cc_final: 0.8766 (t0) REVERT: B 76 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7647 (mmmt) REVERT: B 82 ASP cc_start: 0.6963 (p0) cc_final: 0.6555 (p0) REVERT: P 17 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8294 (mmmm) REVERT: R 82 ASP cc_start: 0.8632 (p0) cc_final: 0.8085 (p0) REVERT: T 82 ASP cc_start: 0.9032 (p0) cc_final: 0.8329 (p0) REVERT: T 93 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8233 (mtpp) REVERT: V 80 ASP cc_start: 0.8301 (m-30) cc_final: 0.8094 (m-30) REVERT: V 82 ASP cc_start: 0.8669 (p0) cc_final: 0.8213 (p0) REVERT: V 93 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8245 (mtpp) REVERT: H 21 ASN cc_start: 0.8384 (t0) cc_final: 0.8008 (t0) REVERT: H 79 SER cc_start: 0.8643 (p) cc_final: 0.8439 (p) REVERT: H 104 GLN cc_start: 0.7798 (pm20) cc_final: 0.6914 (pp30) REVERT: J 13 ASP cc_start: 0.8075 (t70) cc_final: 0.7829 (t70) REVERT: L 16 PHE cc_start: 0.8334 (t80) cc_final: 0.7823 (t80) REVERT: N 67 TYR cc_start: 0.9102 (p90) cc_final: 0.8819 (p90) REVERT: N 93 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7937 (mtpp) REVERT: F 73 TRP cc_start: 0.8110 (p90) cc_final: 0.7736 (p90) REVERT: X 61 ASN cc_start: 0.8354 (p0) cc_final: 0.7715 (t0) REVERT: X 80 ASP cc_start: 0.8848 (m-30) cc_final: 0.8571 (m-30) REVERT: X 93 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8600 (mmmm) REVERT: Z 66 TRP cc_start: 0.8475 (m100) cc_final: 0.7975 (m100) REVERT: Z 93 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8632 (mmmm) REVERT: Z 101 TRP cc_start: 0.7091 (p90) cc_final: 0.6858 (p-90) REVERT: 1 67 TYR cc_start: 0.8531 (p90) cc_final: 0.8019 (p90) REVERT: 1 82 ASP cc_start: 0.8649 (p0) cc_final: 0.8076 (p0) REVERT: 1 101 TRP cc_start: 0.6986 (p90) cc_final: 0.6746 (p90) REVERT: 3 17 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7713 (mmmm) REVERT: 3 21 ASN cc_start: 0.8948 (t0) cc_final: 0.8585 (t0) REVERT: 3 82 ASP cc_start: 0.8077 (p0) cc_final: 0.7057 (p0) REVERT: 5 21 ASN cc_start: 0.8964 (t0) cc_final: 0.8593 (t0) REVERT: 5 42 ASP cc_start: 0.7735 (m-30) cc_final: 0.7498 (m-30) REVERT: 5 49 ASN cc_start: 0.8869 (t0) cc_final: 0.8668 (t0) REVERT: 5 68 ILE cc_start: 0.8319 (mt) cc_final: 0.8071 (tp) REVERT: 5 82 ASP cc_start: 0.8270 (p0) cc_final: 0.7214 (p0) REVERT: 5 93 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8683 (mmmm) outliers start: 0 outliers final: 0 residues processed: 945 average time/residue: 0.1367 time to fit residues: 197.6998 Evaluate side-chains 641 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 641 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 ASN S 33 ASN U 33 ASN E 33 ASN ** Y 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 ASN 4 33 ASN D 30 ASN D 40 ASN B 46 ASN B 70 ASN P 21 ASN P 60 ASN R 30 ASN L 61 ASN L 64 ASN N 21 ASN N 64 ASN F 21 ASN F 30 ASN Z 21 ASN 5 104 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.109540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087291 restraints weight = 36410.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090161 restraints weight = 19841.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092049 restraints weight = 13580.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093301 restraints weight = 10684.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094114 restraints weight = 9155.136| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20176 Z= 0.178 Angle : 0.679 8.863 27504 Z= 0.377 Chirality : 0.044 0.204 3248 Planarity : 0.005 0.056 3520 Dihedral : 8.917 81.825 2784 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.19 % Allowed : 18.06 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2576 helix: -1.10 (0.19), residues: 736 sheet: 0.23 (0.23), residues: 304 loop : -2.30 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 28 TYR 0.018 0.002 TYR 3 67 PHE 0.025 0.003 PHE X 14 TRP 0.024 0.002 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00398 (20176) covalent geometry : angle 0.67899 (27504) hydrogen bonds : bond 0.06875 ( 624) hydrogen bonds : angle 5.76868 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 700 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8602 (t80) cc_final: 0.8246 (t80) REVERT: O 19 ILE cc_start: 0.8127 (mt) cc_final: 0.7858 (mm) REVERT: O 55 GLN cc_start: 0.8675 (mp10) cc_final: 0.8470 (mp10) REVERT: S 28 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7669 (ttm170) REVERT: G 25 SER cc_start: 0.8869 (m) cc_final: 0.8525 (p) REVERT: G 42 ASN cc_start: 0.8505 (t0) cc_final: 0.8262 (m-40) REVERT: I 34 SER cc_start: 0.9222 (m) cc_final: 0.8740 (t) REVERT: I 51 PHE cc_start: 0.8855 (t80) cc_final: 0.8319 (t80) REVERT: K 34 SER cc_start: 0.9121 (m) cc_final: 0.8695 (t) REVERT: K 55 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8284 (mp10) REVERT: M 55 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8273 (mm-40) REVERT: C 51 PHE cc_start: 0.8855 (t80) cc_final: 0.8232 (t80) REVERT: E 25 SER cc_start: 0.8983 (m) cc_final: 0.8620 (t) REVERT: E 41 ARG cc_start: 0.8879 (tmt-80) cc_final: 0.8651 (tmt170) REVERT: E 51 PHE cc_start: 0.8741 (t80) cc_final: 0.8149 (t80) REVERT: W 48 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7915 (tm-30) REVERT: Y 41 ARG cc_start: 0.8565 (tmt-80) cc_final: 0.7467 (ttp-170) REVERT: Y 48 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8019 (tm-30) REVERT: Y 55 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8463 (mp10) REVERT: 0 25 SER cc_start: 0.9270 (m) cc_final: 0.8852 (p) REVERT: 0 41 ARG cc_start: 0.8624 (tmt-80) cc_final: 0.7361 (ttp-170) REVERT: 2 28 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7706 (tpt170) REVERT: 4 10 VAL cc_start: 0.9611 (m) cc_final: 0.9366 (t) REVERT: 4 19 ILE cc_start: 0.8605 (mm) cc_final: 0.8376 (mm) REVERT: 4 41 ARG cc_start: 0.8852 (tmt-80) cc_final: 0.7416 (ttp-170) REVERT: 4 48 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8296 (tm-30) REVERT: D 16 PHE cc_start: 0.7749 (t80) cc_final: 0.7488 (t80) REVERT: D 56 PHE cc_start: 0.9062 (m-80) cc_final: 0.8769 (m-80) REVERT: D 76 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8106 (mmmm) REVERT: B 17 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8543 (mmmt) REVERT: B 21 ASN cc_start: 0.8788 (t0) cc_final: 0.8554 (t0) REVERT: B 76 LYS cc_start: 0.8351 (mmtt) cc_final: 0.7905 (mmmt) REVERT: P 17 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8437 (mmmm) REVERT: P 101 TRP cc_start: 0.6553 (p-90) cc_final: 0.6277 (p-90) REVERT: R 21 ASN cc_start: 0.8146 (t0) cc_final: 0.7901 (t0) REVERT: R 101 TRP cc_start: 0.6884 (p-90) cc_final: 0.6527 (p-90) REVERT: T 42 ASP cc_start: 0.8350 (m-30) cc_final: 0.8147 (m-30) REVERT: V 17 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7868 (mmmm) REVERT: V 69 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7987 (tm-30) REVERT: J 13 ASP cc_start: 0.7959 (t70) cc_final: 0.7744 (t70) REVERT: L 73 TRP cc_start: 0.7837 (p90) cc_final: 0.7381 (p90) REVERT: F 15 THR cc_start: 0.7819 (t) cc_final: 0.7591 (p) REVERT: F 73 TRP cc_start: 0.8185 (p90) cc_final: 0.7894 (p90) REVERT: X 17 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8191 (mmmm) REVERT: X 61 ASN cc_start: 0.8366 (p0) cc_final: 0.7505 (t0) REVERT: X 93 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8487 (mmmm) REVERT: Z 42 ASP cc_start: 0.8254 (t70) cc_final: 0.7958 (t0) REVERT: Z 93 LYS cc_start: 0.8641 (mmmm) cc_final: 0.8436 (mtpp) REVERT: Z 104 GLN cc_start: 0.6923 (pp30) cc_final: 0.6621 (pp30) REVERT: 1 12 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8803 (mmmm) REVERT: 1 17 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8372 (mmmm) REVERT: 1 21 ASN cc_start: 0.8564 (t0) cc_final: 0.8272 (t0) REVERT: 1 42 ASP cc_start: 0.8214 (t0) cc_final: 0.7872 (t0) REVERT: 1 90 ASP cc_start: 0.8148 (p0) cc_final: 0.7819 (p0) REVERT: 1 93 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8324 (mttt) REVERT: 1 101 TRP cc_start: 0.6872 (p90) cc_final: 0.6588 (p90) REVERT: 3 17 LYS cc_start: 0.8631 (mmtt) cc_final: 0.7950 (mmmm) REVERT: 3 42 ASP cc_start: 0.8110 (t0) cc_final: 0.7691 (t70) REVERT: 3 93 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8561 (mtpt) REVERT: 5 21 ASN cc_start: 0.9069 (t0) cc_final: 0.8223 (t0) REVERT: 5 68 ILE cc_start: 0.8201 (mt) cc_final: 0.7976 (tp) REVERT: 5 82 ASP cc_start: 0.8266 (p0) cc_final: 0.7830 (p0) outliers start: 69 outliers final: 39 residues processed: 723 average time/residue: 0.1345 time to fit residues: 148.0810 Evaluate side-chains 626 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 587 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 76 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 201 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN 0 23 GLN 2 33 ASN D 40 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 60 ASN ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN J 21 ASN J 61 ASN L 61 ASN N 64 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.084432 restraints weight = 36830.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087468 restraints weight = 19241.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089447 restraints weight = 12747.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090714 restraints weight = 9847.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091539 restraints weight = 8386.714| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20176 Z= 0.198 Angle : 0.654 9.310 27504 Z= 0.355 Chirality : 0.045 0.217 3248 Planarity : 0.005 0.041 3520 Dihedral : 8.320 84.480 2784 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 3.70 % Allowed : 19.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.17), residues: 2576 helix: -0.33 (0.21), residues: 736 sheet: 0.25 (0.25), residues: 304 loop : -2.05 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 28 TYR 0.024 0.002 TYR X 43 PHE 0.018 0.002 PHE X 14 TRP 0.020 0.002 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00458 (20176) covalent geometry : angle 0.65420 (27504) hydrogen bonds : bond 0.06009 ( 624) hydrogen bonds : angle 5.35636 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 634 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8610 (t80) cc_final: 0.8255 (t80) REVERT: O 19 ILE cc_start: 0.8185 (mt) cc_final: 0.7971 (mt) REVERT: O 55 GLN cc_start: 0.8718 (mp10) cc_final: 0.8512 (mp10) REVERT: Q 23 GLN cc_start: 0.8041 (mp10) cc_final: 0.7753 (mp10) REVERT: S 28 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7304 (ttm170) REVERT: G 25 SER cc_start: 0.9006 (m) cc_final: 0.8570 (p) REVERT: I 24 PHE cc_start: 0.8931 (m-10) cc_final: 0.8686 (m-80) REVERT: I 34 SER cc_start: 0.9270 (m) cc_final: 0.8824 (t) REVERT: I 51 PHE cc_start: 0.8884 (t80) cc_final: 0.8457 (t80) REVERT: K 7 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8943 (mp) REVERT: K 51 PHE cc_start: 0.9010 (t80) cc_final: 0.8629 (t80) REVERT: K 55 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8252 (mp10) REVERT: M 55 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8329 (mm-40) REVERT: C 51 PHE cc_start: 0.8777 (t80) cc_final: 0.8160 (t80) REVERT: E 25 SER cc_start: 0.9040 (m) cc_final: 0.8705 (t) REVERT: E 42 ASN cc_start: 0.8664 (t0) cc_final: 0.8330 (m-40) REVERT: E 51 PHE cc_start: 0.8730 (t80) cc_final: 0.8241 (t80) REVERT: W 48 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8040 (tm-30) REVERT: Y 41 ARG cc_start: 0.8669 (tmt-80) cc_final: 0.7414 (ttp-170) REVERT: Y 48 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8156 (tm-30) REVERT: 0 25 SER cc_start: 0.9305 (m) cc_final: 0.8962 (p) REVERT: 2 28 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7568 (tpt170) REVERT: 2 47 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8707 (mp) REVERT: 4 19 ILE cc_start: 0.8628 (mm) cc_final: 0.8383 (mm) REVERT: 4 48 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8375 (tm-30) REVERT: D 42 ASP cc_start: 0.8488 (t0) cc_final: 0.7809 (t70) REVERT: D 76 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8036 (mmmm) REVERT: B 42 ASP cc_start: 0.8537 (t0) cc_final: 0.8124 (t0) REVERT: B 43 TYR cc_start: 0.8941 (p90) cc_final: 0.8610 (p90) REVERT: B 76 LYS cc_start: 0.8371 (mmtt) cc_final: 0.7987 (mmmt) REVERT: P 17 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8446 (mmmm) REVERT: R 21 ASN cc_start: 0.8304 (t0) cc_final: 0.8007 (t0) REVERT: T 42 ASP cc_start: 0.8473 (m-30) cc_final: 0.8273 (m-30) REVERT: T 93 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8516 (mtpp) REVERT: V 17 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8150 (mmmt) REVERT: V 69 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8053 (tm-30) REVERT: V 93 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8428 (mtpp) REVERT: H 21 ASN cc_start: 0.8312 (t0) cc_final: 0.8082 (t0) REVERT: H 42 ASP cc_start: 0.8410 (t70) cc_final: 0.8079 (t70) REVERT: J 13 ASP cc_start: 0.7932 (t70) cc_final: 0.7629 (t70) REVERT: J 42 ASP cc_start: 0.8534 (t70) cc_final: 0.8296 (t0) REVERT: L 69 GLU cc_start: 0.7809 (tt0) cc_final: 0.7561 (tt0) REVERT: N 17 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8362 (mptt) REVERT: N 43 TYR cc_start: 0.8982 (p90) cc_final: 0.8735 (p90) REVERT: F 17 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8637 (mmtp) REVERT: F 73 TRP cc_start: 0.8307 (p90) cc_final: 0.7857 (p90) REVERT: X 17 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8542 (mmmm) REVERT: X 93 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8391 (mmmm) REVERT: Z 42 ASP cc_start: 0.8386 (t70) cc_final: 0.8130 (t70) REVERT: Z 104 GLN cc_start: 0.7090 (pp30) cc_final: 0.6816 (pp30) REVERT: 1 12 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8852 (mmmm) REVERT: 1 17 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8490 (mmmm) REVERT: 1 21 ASN cc_start: 0.8768 (t0) cc_final: 0.8341 (t0) REVERT: 1 42 ASP cc_start: 0.8430 (t70) cc_final: 0.8058 (t0) REVERT: 1 74 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8697 (ttmt) REVERT: 1 93 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8393 (mtpt) REVERT: 1 101 TRP cc_start: 0.7073 (p90) cc_final: 0.6861 (p90) REVERT: 3 17 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8106 (mmmm) REVERT: 3 21 ASN cc_start: 0.9102 (t0) cc_final: 0.8808 (t0) REVERT: 3 42 ASP cc_start: 0.8251 (t70) cc_final: 0.7982 (t70) REVERT: 3 69 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8113 (tm-30) REVERT: 3 93 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8680 (mtpt) REVERT: 5 17 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7892 (mmmm) REVERT: 5 21 ASN cc_start: 0.9049 (t0) cc_final: 0.8377 (t0) REVERT: 5 68 ILE cc_start: 0.8252 (mt) cc_final: 0.7948 (tp) outliers start: 80 outliers final: 63 residues processed: 662 average time/residue: 0.1415 time to fit residues: 143.2346 Evaluate side-chains 649 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 584 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 4 residue 37 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 78 VAL Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 78 VAL Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 235 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 33 ASN D 40 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 ASN N 64 ASN ** X 61 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 = 0.3698 r_free = 0.3698 target = 0.109022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086193 restraints weight = 36696.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089184 restraints weight = 20028.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091135 restraints weight = 13633.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092311 restraints weight = 10694.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093164 restraints weight = 9229.388| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20176 Z= 0.158 Angle : 0.615 9.695 27504 Z= 0.334 Chirality : 0.043 0.209 3248 Planarity : 0.004 0.036 3520 Dihedral : 7.840 87.190 2784 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.21 % Allowed : 20.09 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2576 helix: 0.05 (0.21), residues: 736 sheet: 0.27 (0.26), residues: 304 loop : -1.91 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 28 TYR 0.020 0.002 TYR 3 43 PHE 0.028 0.002 PHE X 14 TRP 0.017 0.002 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00360 (20176) covalent geometry : angle 0.61525 (27504) hydrogen bonds : bond 0.05339 ( 624) hydrogen bonds : angle 4.99244 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 647 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8482 (t80) cc_final: 0.8024 (t80) REVERT: Q 28 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7488 (ttp80) REVERT: Q 53 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8412 (t0) REVERT: U 53 ASP cc_start: 0.8560 (m-30) cc_final: 0.8080 (t0) REVERT: G 25 SER cc_start: 0.8981 (m) cc_final: 0.8623 (t) REVERT: G 42 ASN cc_start: 0.8682 (m-40) cc_final: 0.8404 (m-40) REVERT: I 24 PHE cc_start: 0.8847 (m-10) cc_final: 0.8632 (m-80) REVERT: I 51 PHE cc_start: 0.8764 (t80) cc_final: 0.8269 (t80) REVERT: K 51 PHE cc_start: 0.8870 (t80) cc_final: 0.8458 (t80) REVERT: K 55 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8338 (mp10) REVERT: C 51 PHE cc_start: 0.8664 (t80) cc_final: 0.7960 (t80) REVERT: E 25 SER cc_start: 0.8988 (m) cc_final: 0.8640 (t) REVERT: E 42 ASN cc_start: 0.8595 (t0) cc_final: 0.8294 (m-40) REVERT: E 51 PHE cc_start: 0.8527 (t80) cc_final: 0.8018 (t80) REVERT: W 48 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8048 (tm-30) REVERT: W 55 GLN cc_start: 0.8840 (mp10) cc_final: 0.8531 (mp10) REVERT: Y 41 ARG cc_start: 0.8741 (tmt-80) cc_final: 0.7424 (ttp-170) REVERT: 0 25 SER cc_start: 0.9292 (m) cc_final: 0.8949 (p) REVERT: 2 28 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7493 (tpt170) REVERT: 4 19 ILE cc_start: 0.8720 (mm) cc_final: 0.8448 (mm) REVERT: 4 48 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8417 (tm-30) REVERT: D 42 ASP cc_start: 0.8546 (t70) cc_final: 0.7816 (t0) REVERT: D 76 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8107 (mmmm) REVERT: B 17 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8324 (mmmt) REVERT: B 26 TYR cc_start: 0.8664 (t80) cc_final: 0.8438 (t80) REVERT: B 42 ASP cc_start: 0.8579 (t0) cc_final: 0.8101 (t0) REVERT: B 76 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7973 (mmmt) REVERT: P 17 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8483 (mmmm) REVERT: P 101 TRP cc_start: 0.6445 (p-90) cc_final: 0.6228 (p-90) REVERT: R 21 ASN cc_start: 0.8203 (t0) cc_final: 0.7927 (t0) REVERT: R 101 TRP cc_start: 0.6930 (p-90) cc_final: 0.6668 (p-90) REVERT: T 93 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8406 (mtpp) REVERT: V 93 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8353 (mtpp) REVERT: H 42 ASP cc_start: 0.8494 (t70) cc_final: 0.8126 (t70) REVERT: H 104 GLN cc_start: 0.7432 (pm20) cc_final: 0.6996 (pp30) REVERT: L 69 GLU cc_start: 0.7675 (tt0) cc_final: 0.7392 (tt0) REVERT: N 17 LYS cc_start: 0.8915 (mmmm) cc_final: 0.8522 (mptt) REVERT: N 67 TYR cc_start: 0.8955 (p90) cc_final: 0.8752 (p90) REVERT: F 17 LYS cc_start: 0.8945 (mmtp) cc_final: 0.8721 (mmtp) REVERT: F 73 TRP cc_start: 0.8214 (p90) cc_final: 0.7920 (p90) REVERT: X 17 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8684 (mmmm) REVERT: X 104 GLN cc_start: 0.7701 (pm20) cc_final: 0.7175 (pp30) REVERT: Z 104 GLN cc_start: 0.7014 (pp30) cc_final: 0.6524 (pp30) REVERT: 1 12 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8783 (mmmm) REVERT: 1 17 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8539 (mmmm) REVERT: 1 21 ASN cc_start: 0.8704 (t0) cc_final: 0.8249 (t0) REVERT: 1 42 ASP cc_start: 0.8457 (t70) cc_final: 0.8091 (t0) REVERT: 1 93 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8294 (mtpt) REVERT: 3 17 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8208 (mmmm) REVERT: 3 21 ASN cc_start: 0.9052 (t0) cc_final: 0.8654 (t0) REVERT: 3 42 ASP cc_start: 0.8358 (t70) cc_final: 0.8010 (t70) REVERT: 3 69 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7907 (tm-30) REVERT: 3 93 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8623 (mtpt) REVERT: 5 17 LYS cc_start: 0.8507 (mmtt) cc_final: 0.7968 (mmmm) REVERT: 5 21 ASN cc_start: 0.8981 (t0) cc_final: 0.8333 (t0) REVERT: 5 68 ILE cc_start: 0.8070 (mt) cc_final: 0.7841 (tp) REVERT: 5 104 GLN cc_start: 0.3154 (mm-40) cc_final: 0.2905 (mm-40) outliers start: 91 outliers final: 67 residues processed: 679 average time/residue: 0.1379 time to fit residues: 144.1165 Evaluate side-chains 652 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 584 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain X residue 13 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 48 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 189 optimal weight: 0.0970 chunk 198 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 33 ASN D 40 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN F 21 ASN ** X 61 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 = 0.3717 r_free = 0.3717 target = 0.110436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.087659 restraints weight = 36056.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090821 restraints weight = 18800.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092846 restraints weight = 12427.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094104 restraints weight = 9585.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095030 restraints weight = 8171.494| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20176 Z= 0.142 Angle : 0.605 9.446 27504 Z= 0.327 Chirality : 0.043 0.210 3248 Planarity : 0.004 0.061 3520 Dihedral : 7.411 89.616 2784 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.58 % Allowed : 21.30 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2576 helix: 0.34 (0.21), residues: 736 sheet: 0.33 (0.27), residues: 304 loop : -1.87 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 28 TYR 0.024 0.002 TYR 3 43 PHE 0.025 0.002 PHE F 14 TRP 0.016 0.001 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00322 (20176) covalent geometry : angle 0.60533 (27504) hydrogen bonds : bond 0.04866 ( 624) hydrogen bonds : angle 4.77996 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 640 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8023 (ttp80) REVERT: A 32 TYR cc_start: 0.8929 (m-80) cc_final: 0.8728 (m-80) REVERT: A 51 PHE cc_start: 0.8430 (t80) cc_final: 0.7914 (t80) REVERT: Q 28 ARG cc_start: 0.7697 (ttp-110) cc_final: 0.7335 (ttp80) REVERT: S 28 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7294 (ttm170) REVERT: U 28 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7126 (ptt90) REVERT: U 53 ASP cc_start: 0.8465 (m-30) cc_final: 0.8023 (t0) REVERT: U 54 ASP cc_start: 0.7888 (m-30) cc_final: 0.7635 (m-30) REVERT: G 25 SER cc_start: 0.8978 (m) cc_final: 0.8603 (p) REVERT: G 42 ASN cc_start: 0.8604 (m-40) cc_final: 0.8318 (m-40) REVERT: I 51 PHE cc_start: 0.8632 (t80) cc_final: 0.8137 (t80) REVERT: K 51 PHE cc_start: 0.8726 (t80) cc_final: 0.8260 (t80) REVERT: K 55 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8328 (mp10) REVERT: C 51 PHE cc_start: 0.8546 (t80) cc_final: 0.7909 (t80) REVERT: E 25 SER cc_start: 0.8942 (m) cc_final: 0.8603 (t) REVERT: E 42 ASN cc_start: 0.8568 (t0) cc_final: 0.8345 (m-40) REVERT: E 51 PHE cc_start: 0.8396 (t80) cc_final: 0.7845 (t80) REVERT: W 48 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7974 (tm-30) REVERT: W 55 GLN cc_start: 0.8766 (mp10) cc_final: 0.8537 (mp10) REVERT: 0 25 SER cc_start: 0.9181 (m) cc_final: 0.8913 (p) REVERT: 2 28 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7422 (tpt170) REVERT: D 42 ASP cc_start: 0.8497 (t70) cc_final: 0.7765 (t0) REVERT: D 76 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8110 (mmmm) REVERT: B 13 ASP cc_start: 0.8310 (p0) cc_final: 0.7573 (t70) REVERT: B 17 LYS cc_start: 0.8949 (mmtp) cc_final: 0.8330 (mmmt) REVERT: B 42 ASP cc_start: 0.8557 (t0) cc_final: 0.8012 (t0) REVERT: B 76 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8023 (mmtp) REVERT: P 17 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8572 (mmmm) REVERT: P 101 TRP cc_start: 0.6424 (p-90) cc_final: 0.6219 (p-90) REVERT: R 21 ASN cc_start: 0.8139 (t0) cc_final: 0.7872 (t0) REVERT: R 101 TRP cc_start: 0.6932 (p-90) cc_final: 0.6682 (p-90) REVERT: T 93 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8473 (mtpp) REVERT: V 93 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8291 (mtpp) REVERT: H 42 ASP cc_start: 0.8488 (t70) cc_final: 0.8110 (t70) REVERT: H 104 GLN cc_start: 0.7432 (pm20) cc_final: 0.7080 (pp30) REVERT: L 13 ASP cc_start: 0.8838 (p0) cc_final: 0.8584 (p0) REVERT: N 17 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8598 (mptt) REVERT: N 61 ASN cc_start: 0.8589 (t0) cc_final: 0.8176 (p0) REVERT: F 42 ASP cc_start: 0.8406 (t70) cc_final: 0.8162 (t70) REVERT: X 17 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8672 (mmmm) REVERT: Z 93 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8048 (mtpp) REVERT: Z 104 GLN cc_start: 0.6964 (pp30) cc_final: 0.6401 (pp30) REVERT: 1 12 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8746 (mmmm) REVERT: 1 17 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8594 (mmmm) REVERT: 1 21 ASN cc_start: 0.8700 (t0) cc_final: 0.8266 (t0) REVERT: 1 42 ASP cc_start: 0.8472 (t70) cc_final: 0.8134 (t0) REVERT: 1 93 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8383 (mttt) REVERT: 3 17 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8347 (mmmm) REVERT: 3 21 ASN cc_start: 0.9040 (t0) cc_final: 0.8649 (t0) REVERT: 3 42 ASP cc_start: 0.8429 (t70) cc_final: 0.8095 (t0) REVERT: 3 54 ARG cc_start: 0.9055 (mtp180) cc_final: 0.8659 (mtt180) REVERT: 3 69 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7791 (tm-30) REVERT: 3 93 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8599 (mtpt) REVERT: 5 17 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8020 (mmmm) REVERT: 5 21 ASN cc_start: 0.8955 (t0) cc_final: 0.8326 (t0) REVERT: 5 68 ILE cc_start: 0.8018 (mt) cc_final: 0.7794 (tp) REVERT: 5 104 GLN cc_start: 0.3073 (mm-40) cc_final: 0.2830 (mm-40) outliers start: 99 outliers final: 78 residues processed: 679 average time/residue: 0.1331 time to fit residues: 139.8214 Evaluate side-chains 673 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 595 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain S residue 60 GLU Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 15 ILE Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain T residue 41 THR Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 46 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 199 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 204 optimal weight: 0.0270 chunk 224 optimal weight: 3.9990 chunk 181 optimal weight: 0.2980 chunk 230 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN B 46 ASN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.112974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.089742 restraints weight = 35811.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092872 restraints weight = 19370.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.094893 restraints weight = 13095.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096198 restraints weight = 10243.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096980 restraints weight = 8762.629| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20176 Z= 0.133 Angle : 0.602 9.162 27504 Z= 0.323 Chirality : 0.042 0.209 3248 Planarity : 0.004 0.054 3520 Dihedral : 6.983 89.419 2784 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 4.54 % Allowed : 21.94 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2576 helix: 0.49 (0.20), residues: 752 sheet: -0.15 (0.26), residues: 400 loop : -1.77 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG W 28 TYR 0.027 0.002 TYR X 26 PHE 0.028 0.002 PHE J 27 TRP 0.013 0.001 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00296 (20176) covalent geometry : angle 0.60218 (27504) hydrogen bonds : bond 0.04497 ( 624) hydrogen bonds : angle 4.64016 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 645 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 28 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7104 (ttm170) REVERT: U 4 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8295 (tp) REVERT: U 28 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7088 (ptt90) REVERT: U 48 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: U 53 ASP cc_start: 0.8387 (m-30) cc_final: 0.8142 (t0) REVERT: U 60 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: G 25 SER cc_start: 0.8879 (m) cc_final: 0.8520 (p) REVERT: I 51 PHE cc_start: 0.8534 (t80) cc_final: 0.7891 (t80) REVERT: I 56 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8181 (t) REVERT: K 7 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8846 (mp) REVERT: K 51 PHE cc_start: 0.8541 (t80) cc_final: 0.8193 (t80) REVERT: K 55 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8295 (mp10) REVERT: C 51 PHE cc_start: 0.8507 (t80) cc_final: 0.8243 (t80) REVERT: E 51 PHE cc_start: 0.8283 (t80) cc_final: 0.7822 (t80) REVERT: E 55 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: Y 48 GLU cc_start: 0.8242 (tp30) cc_final: 0.7955 (tm-30) REVERT: 0 25 SER cc_start: 0.9133 (m) cc_final: 0.8902 (p) REVERT: 2 28 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7348 (tpt170) REVERT: D 42 ASP cc_start: 0.8481 (t70) cc_final: 0.7726 (t0) REVERT: D 76 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8077 (mmmm) REVERT: B 13 ASP cc_start: 0.8233 (p0) cc_final: 0.7525 (t70) REVERT: B 17 LYS cc_start: 0.8941 (mmtp) cc_final: 0.8738 (mmtp) REVERT: B 42 ASP cc_start: 0.8491 (t0) cc_final: 0.7901 (t0) REVERT: B 76 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8029 (mmtp) REVERT: P 17 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8652 (mmmm) REVERT: R 21 ASN cc_start: 0.8041 (t0) cc_final: 0.7806 (t0) REVERT: R 101 TRP cc_start: 0.6935 (p-90) cc_final: 0.6707 (p-90) REVERT: T 42 ASP cc_start: 0.8236 (m-30) cc_final: 0.7907 (t0) REVERT: V 93 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8216 (mtpp) REVERT: H 42 ASP cc_start: 0.8473 (t70) cc_final: 0.8069 (t70) REVERT: H 104 GLN cc_start: 0.7395 (pm20) cc_final: 0.7086 (pp30) REVERT: L 61 ASN cc_start: 0.8820 (t0) cc_final: 0.8300 (p0) REVERT: N 17 LYS cc_start: 0.9043 (mmmm) cc_final: 0.8675 (mptt) REVERT: N 61 ASN cc_start: 0.8549 (t0) cc_final: 0.8172 (p0) REVERT: F 42 ASP cc_start: 0.8449 (t70) cc_final: 0.7781 (t70) REVERT: Z 21 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8017 (t0) REVERT: Z 93 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8025 (mtpp) REVERT: Z 104 GLN cc_start: 0.6970 (pp30) cc_final: 0.6391 (pp30) REVERT: 1 12 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8770 (mmmm) REVERT: 1 17 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8661 (mmmm) REVERT: 1 21 ASN cc_start: 0.8692 (t0) cc_final: 0.8381 (t0) REVERT: 1 42 ASP cc_start: 0.8536 (t70) cc_final: 0.8177 (t0) REVERT: 1 93 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8419 (mttt) REVERT: 3 17 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8440 (mmmm) REVERT: 3 21 ASN cc_start: 0.8982 (t0) cc_final: 0.8663 (t0) REVERT: 3 26 TYR cc_start: 0.8096 (t80) cc_final: 0.7869 (t80) REVERT: 3 42 ASP cc_start: 0.8445 (t70) cc_final: 0.8146 (t0) REVERT: 3 69 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7671 (tm-30) REVERT: 3 93 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8561 (mtpt) REVERT: 5 17 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8004 (mmmm) REVERT: 5 21 ASN cc_start: 0.8945 (t0) cc_final: 0.8303 (t0) REVERT: 5 68 ILE cc_start: 0.7953 (mt) cc_final: 0.7728 (tp) outliers start: 98 outliers final: 70 residues processed: 681 average time/residue: 0.1395 time to fit residues: 146.5527 Evaluate side-chains 659 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 582 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 46 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 42 optimal weight: 0.0570 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090634 restraints weight = 35673.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093917 restraints weight = 18276.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.096041 restraints weight = 11946.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097358 restraints weight = 9160.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098334 restraints weight = 7766.024| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20176 Z= 0.138 Angle : 0.619 8.463 27504 Z= 0.332 Chirality : 0.042 0.181 3248 Planarity : 0.004 0.048 3520 Dihedral : 6.689 87.822 2784 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.40 % Allowed : 23.56 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2576 helix: 0.72 (0.20), residues: 752 sheet: -0.30 (0.25), residues: 400 loop : -1.78 (0.18), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 28 TYR 0.026 0.002 TYR Z 26 PHE 0.039 0.002 PHE H 14 TRP 0.015 0.001 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00313 (20176) covalent geometry : angle 0.61883 (27504) hydrogen bonds : bond 0.04337 ( 624) hydrogen bonds : angle 4.56520 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 626 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7927 (ttp80) REVERT: Q 28 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7040 (ttp80) REVERT: S 28 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7235 (ttm170) REVERT: S 44 LYS cc_start: 0.8936 (tttt) cc_final: 0.8515 (mttt) REVERT: U 28 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7050 (ptt90) REVERT: U 48 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: U 53 ASP cc_start: 0.8339 (m-30) cc_final: 0.8108 (t0) REVERT: G 25 SER cc_start: 0.8910 (m) cc_final: 0.8499 (p) REVERT: I 51 PHE cc_start: 0.8379 (t80) cc_final: 0.7893 (t80) REVERT: K 7 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8914 (mp) REVERT: K 51 PHE cc_start: 0.8470 (t80) cc_final: 0.8240 (t80) REVERT: K 55 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8306 (mp10) REVERT: C 51 PHE cc_start: 0.8464 (t80) cc_final: 0.8215 (t80) REVERT: E 51 PHE cc_start: 0.8273 (t80) cc_final: 0.7815 (t80) REVERT: E 55 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (mm-40) REVERT: Y 48 GLU cc_start: 0.8204 (tp30) cc_final: 0.7979 (tm-30) REVERT: 2 28 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7281 (tpt170) REVERT: 2 60 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 42 ASP cc_start: 0.8479 (t70) cc_final: 0.7771 (t0) REVERT: D 76 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8098 (mmmm) REVERT: B 13 ASP cc_start: 0.8238 (p0) cc_final: 0.7558 (t70) REVERT: B 17 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8748 (mmtp) REVERT: B 27 PHE cc_start: 0.8447 (m-80) cc_final: 0.7824 (m-10) REVERT: B 42 ASP cc_start: 0.8442 (t0) cc_final: 0.7856 (t0) REVERT: P 17 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8682 (mmmm) REVERT: R 21 ASN cc_start: 0.8078 (t0) cc_final: 0.7818 (t0) REVERT: R 43 TYR cc_start: 0.8537 (p90) cc_final: 0.8173 (p90) REVERT: R 101 TRP cc_start: 0.6949 (p-90) cc_final: 0.6729 (p-90) REVERT: T 42 ASP cc_start: 0.8231 (m-30) cc_final: 0.7887 (t0) REVERT: V 9 MET cc_start: 0.8396 (mmt) cc_final: 0.8054 (mmp) REVERT: H 26 TYR cc_start: 0.8463 (t80) cc_final: 0.8184 (t80) REVERT: H 42 ASP cc_start: 0.8606 (t70) cc_final: 0.8064 (t0) REVERT: H 104 GLN cc_start: 0.7397 (pm20) cc_final: 0.7092 (pp30) REVERT: L 61 ASN cc_start: 0.8846 (t0) cc_final: 0.8280 (p0) REVERT: N 17 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8677 (mptt) REVERT: N 61 ASN cc_start: 0.8601 (t0) cc_final: 0.8238 (p0) REVERT: F 42 ASP cc_start: 0.8450 (t70) cc_final: 0.7804 (t70) REVERT: Z 21 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8044 (t0) REVERT: Z 93 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7997 (mtpp) REVERT: 1 12 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8749 (mmmm) REVERT: 1 17 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8625 (mmmm) REVERT: 1 21 ASN cc_start: 0.8697 (t0) cc_final: 0.8390 (t0) REVERT: 1 42 ASP cc_start: 0.8542 (t70) cc_final: 0.8191 (t0) REVERT: 1 93 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8412 (mttt) REVERT: 1 104 GLN cc_start: 0.7547 (pm20) cc_final: 0.7292 (pp30) REVERT: 3 17 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8400 (mmmm) REVERT: 3 21 ASN cc_start: 0.8970 (t0) cc_final: 0.8625 (t0) REVERT: 3 26 TYR cc_start: 0.8023 (t80) cc_final: 0.7772 (t80) REVERT: 3 42 ASP cc_start: 0.8462 (t70) cc_final: 0.8178 (t0) REVERT: 3 54 ARG cc_start: 0.8983 (mtp180) cc_final: 0.8575 (mtt180) REVERT: 3 69 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7622 (tm-30) REVERT: 3 82 ASP cc_start: 0.7752 (p0) cc_final: 0.7018 (t0) REVERT: 3 93 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8530 (mtpt) REVERT: 5 17 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8038 (mmmm) REVERT: 5 21 ASN cc_start: 0.8883 (t0) cc_final: 0.8302 (t0) REVERT: 5 68 ILE cc_start: 0.7993 (mt) cc_final: 0.7770 (tp) outliers start: 95 outliers final: 74 residues processed: 666 average time/residue: 0.1317 time to fit residues: 135.5256 Evaluate side-chains 659 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 581 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 48 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 57 THR Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 46 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 78 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.113744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090433 restraints weight = 36065.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093503 restraints weight = 19793.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095496 restraints weight = 13566.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096757 restraints weight = 10715.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.097540 restraints weight = 9247.991| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20176 Z= 0.148 Angle : 0.635 8.867 27504 Z= 0.340 Chirality : 0.044 0.200 3248 Planarity : 0.004 0.035 3520 Dihedral : 6.422 86.976 2784 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.12 % Favored : 90.84 % Rotamer: Outliers : 4.03 % Allowed : 23.94 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.17), residues: 2576 helix: 0.90 (0.20), residues: 752 sheet: 0.06 (0.27), residues: 304 loop : -1.90 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 54 TYR 0.030 0.002 TYR 3 43 PHE 0.032 0.002 PHE X 27 TRP 0.015 0.001 TRP Z 73 Details of bonding type rmsd covalent geometry : bond 0.00343 (20176) covalent geometry : angle 0.63485 (27504) hydrogen bonds : bond 0.04268 ( 624) hydrogen bonds : angle 4.57870 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 624 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7861 (tm-30) REVERT: S 28 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7191 (ttm170) REVERT: U 53 ASP cc_start: 0.8373 (m-30) cc_final: 0.8129 (t0) REVERT: G 25 SER cc_start: 0.8885 (m) cc_final: 0.8513 (p) REVERT: I 51 PHE cc_start: 0.8363 (t80) cc_final: 0.7763 (t80) REVERT: I 56 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (t) REVERT: K 7 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8858 (mp) REVERT: K 51 PHE cc_start: 0.8449 (t80) cc_final: 0.8190 (t80) REVERT: C 51 PHE cc_start: 0.8426 (t80) cc_final: 0.8210 (t80) REVERT: E 19 ILE cc_start: 0.8829 (mm) cc_final: 0.8590 (mm) REVERT: E 51 PHE cc_start: 0.8269 (t80) cc_final: 0.7851 (t80) REVERT: E 55 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: 2 23 GLN cc_start: 0.8164 (pm20) cc_final: 0.7956 (pm20) REVERT: 2 28 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7268 (tpt170) REVERT: 2 60 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7732 (mt-10) REVERT: 4 13 ILE cc_start: 0.9441 (mm) cc_final: 0.9222 (mt) REVERT: D 42 ASP cc_start: 0.8465 (t70) cc_final: 0.7755 (t0) REVERT: D 76 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8096 (mmmm) REVERT: B 13 ASP cc_start: 0.8244 (p0) cc_final: 0.7644 (t70) REVERT: B 17 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8776 (mmtp) REVERT: B 27 PHE cc_start: 0.8517 (m-80) cc_final: 0.8003 (m-10) REVERT: B 42 ASP cc_start: 0.8276 (t0) cc_final: 0.7782 (t0) REVERT: P 17 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8707 (mmmm) REVERT: R 21 ASN cc_start: 0.8036 (t0) cc_final: 0.7817 (t0) REVERT: R 101 TRP cc_start: 0.6949 (p-90) cc_final: 0.6735 (p-90) REVERT: T 42 ASP cc_start: 0.8190 (m-30) cc_final: 0.7906 (t0) REVERT: H 26 TYR cc_start: 0.8461 (t80) cc_final: 0.8216 (t80) REVERT: H 42 ASP cc_start: 0.8528 (t70) cc_final: 0.8064 (t0) REVERT: H 104 GLN cc_start: 0.7388 (pm20) cc_final: 0.7125 (pp30) REVERT: L 61 ASN cc_start: 0.8866 (t0) cc_final: 0.8359 (p0) REVERT: N 17 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8740 (mptt) REVERT: N 61 ASN cc_start: 0.8590 (t0) cc_final: 0.8298 (p0) REVERT: F 42 ASP cc_start: 0.8450 (t70) cc_final: 0.7753 (t70) REVERT: Z 21 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8047 (t0) REVERT: Z 93 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8140 (mtpp) REVERT: 1 12 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8697 (mmmm) REVERT: 1 17 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8714 (mmmm) REVERT: 1 21 ASN cc_start: 0.8697 (t0) cc_final: 0.8391 (t0) REVERT: 1 42 ASP cc_start: 0.8587 (t70) cc_final: 0.8235 (t70) REVERT: 1 93 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8413 (mttt) REVERT: 1 104 GLN cc_start: 0.7554 (pm20) cc_final: 0.7349 (pp30) REVERT: 3 17 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8462 (mmmm) REVERT: 3 21 ASN cc_start: 0.8962 (t0) cc_final: 0.8630 (t0) REVERT: 3 26 TYR cc_start: 0.8116 (t80) cc_final: 0.7862 (t80) REVERT: 3 42 ASP cc_start: 0.8375 (t70) cc_final: 0.8078 (t0) REVERT: 3 82 ASP cc_start: 0.7747 (p0) cc_final: 0.7072 (t0) REVERT: 3 93 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8672 (mmmm) REVERT: 5 17 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8135 (mmmm) REVERT: 5 21 ASN cc_start: 0.8888 (t0) cc_final: 0.8324 (t0) REVERT: 5 68 ILE cc_start: 0.8045 (mt) cc_final: 0.7817 (tp) outliers start: 87 outliers final: 70 residues processed: 662 average time/residue: 0.1381 time to fit residues: 140.5032 Evaluate side-chains 663 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain S residue 21 ILE Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain W residue 19 ILE Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 13 ILE Chi-restraints excluded: chain 2 residue 19 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 29 VAL Chi-restraints excluded: chain 4 residue 37 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain T residue 4 ILE Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 68 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain Z residue 21 ASN Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 46 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 139 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 205 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN 2 33 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 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 = 0.3638 r_free = 0.3638 target = 0.104533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082521 restraints weight = 37423.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.085741 restraints weight = 20826.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087731 restraints weight = 12738.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087697 restraints weight = 10961.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088089 restraints weight = 10304.340| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 20176 Z= 0.307 Angle : 0.771 9.491 27504 Z= 0.411 Chirality : 0.049 0.203 3248 Planarity : 0.005 0.048 3520 Dihedral : 6.528 78.651 2784 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.25 % Favored : 89.71 % Rotamer: Outliers : 4.44 % Allowed : 24.63 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2576 helix: 0.41 (0.20), residues: 752 sheet: -0.61 (0.25), residues: 400 loop : -2.02 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 28 TYR 0.027 0.003 TYR N 26 PHE 0.046 0.003 PHE P 27 TRP 0.024 0.003 TRP 5 73 Details of bonding type rmsd covalent geometry : bond 0.00720 (20176) covalent geometry : angle 0.77121 (27504) hydrogen bonds : bond 0.05340 ( 624) hydrogen bonds : angle 5.04687 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 606 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 4 ILE cc_start: 0.8981 (mt) cc_final: 0.8744 (tp) REVERT: U 28 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7281 (ptt90) REVERT: G 25 SER cc_start: 0.8952 (m) cc_final: 0.8571 (t) REVERT: I 51 PHE cc_start: 0.8645 (t80) cc_final: 0.8254 (t80) REVERT: I 56 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (t) REVERT: C 48 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7909 (tm-30) REVERT: C 51 PHE cc_start: 0.8815 (t80) cc_final: 0.8097 (t80) REVERT: E 25 SER cc_start: 0.8953 (m) cc_final: 0.8621 (t) REVERT: E 51 PHE cc_start: 0.8670 (t80) cc_final: 0.8084 (t80) REVERT: 0 28 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7934 (ttp80) REVERT: 0 30 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8086 (tmtt) REVERT: 2 28 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7570 (tpt170) REVERT: 2 60 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 42 ASP cc_start: 0.8509 (t70) cc_final: 0.7740 (t0) REVERT: B 27 PHE cc_start: 0.8568 (m-80) cc_final: 0.7771 (m-10) REVERT: B 42 ASP cc_start: 0.8359 (t0) cc_final: 0.7766 (t0) REVERT: B 76 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8121 (mmmt) REVERT: P 17 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8725 (mmmm) REVERT: R 21 ASN cc_start: 0.8261 (t0) cc_final: 0.7996 (t0) REVERT: R 101 TRP cc_start: 0.7198 (p-90) cc_final: 0.6957 (p-90) REVERT: T 69 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7853 (tm-30) REVERT: V 88 THR cc_start: 0.8561 (m) cc_final: 0.8329 (m) REVERT: H 42 ASP cc_start: 0.8605 (t70) cc_final: 0.8147 (t70) REVERT: H 43 TYR cc_start: 0.8632 (p90) cc_final: 0.8396 (p90) REVERT: H 93 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8095 (mmmm) REVERT: H 104 GLN cc_start: 0.7534 (pm20) cc_final: 0.7261 (pp30) REVERT: N 17 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8773 (mptt) REVERT: N 61 ASN cc_start: 0.8719 (t0) cc_final: 0.8417 (p0) REVERT: Z 93 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8362 (mmmm) REVERT: 1 17 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8903 (mmmm) REVERT: 1 21 ASN cc_start: 0.8876 (t0) cc_final: 0.8584 (t0) REVERT: 1 42 ASP cc_start: 0.8616 (t70) cc_final: 0.8342 (t70) REVERT: 1 93 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8459 (mttt) REVERT: 3 17 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8606 (mmmm) REVERT: 3 21 ASN cc_start: 0.9053 (t0) cc_final: 0.8751 (t0) REVERT: 3 42 ASP cc_start: 0.8385 (t70) cc_final: 0.8183 (t70) REVERT: 3 69 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7807 (tm-30) REVERT: 3 82 ASP cc_start: 0.7777 (p0) cc_final: 0.7155 (t0) REVERT: 3 93 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8645 (mmmt) REVERT: 5 17 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8303 (mmmm) REVERT: 5 21 ASN cc_start: 0.8931 (t0) cc_final: 0.8294 (t0) REVERT: 5 68 ILE cc_start: 0.8195 (mt) cc_final: 0.7902 (tp) outliers start: 96 outliers final: 78 residues processed: 652 average time/residue: 0.1401 time to fit residues: 140.3184 Evaluate side-chains 653 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 574 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain O residue 37 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 13 ILE Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 2 residue 37 SER Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 37 SER Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 83 VAL Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 192 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.088245 restraints weight = 36147.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091286 restraints weight = 20429.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093470 restraints weight = 12889.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093606 restraints weight = 10652.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094152 restraints weight = 10218.805| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20176 Z= 0.160 Angle : 0.715 9.640 27504 Z= 0.380 Chirality : 0.044 0.233 3248 Planarity : 0.004 0.054 3520 Dihedral : 6.380 78.260 2784 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.24 % Allowed : 26.85 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2576 helix: 0.68 (0.20), residues: 752 sheet: -0.13 (0.27), residues: 304 loop : -2.04 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 28 TYR 0.046 0.003 TYR F 43 PHE 0.033 0.002 PHE N 14 TRP 0.027 0.002 TRP 5 73 Details of bonding type rmsd covalent geometry : bond 0.00368 (20176) covalent geometry : angle 0.71509 (27504) hydrogen bonds : bond 0.04752 ( 624) hydrogen bonds : angle 4.66075 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 604 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 4 ILE cc_start: 0.8883 (mt) cc_final: 0.8548 (tp) REVERT: U 28 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7283 (ptt90) REVERT: G 25 SER cc_start: 0.8925 (m) cc_final: 0.8568 (p) REVERT: I 51 PHE cc_start: 0.8483 (t80) cc_final: 0.8125 (t80) REVERT: I 56 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8327 (t) REVERT: C 51 PHE cc_start: 0.8562 (t80) cc_final: 0.8306 (t80) REVERT: E 25 SER cc_start: 0.8911 (m) cc_final: 0.8528 (t) REVERT: E 51 PHE cc_start: 0.8452 (t80) cc_final: 0.7865 (t80) REVERT: 0 30 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8030 (tmtt) REVERT: 2 28 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7355 (tpt170) REVERT: D 42 ASP cc_start: 0.8529 (t70) cc_final: 0.7799 (t0) REVERT: B 13 ASP cc_start: 0.8278 (p0) cc_final: 0.7656 (t70) REVERT: B 17 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8473 (mmmt) REVERT: B 27 PHE cc_start: 0.8514 (m-80) cc_final: 0.8300 (m-10) REVERT: B 42 ASP cc_start: 0.8319 (t0) cc_final: 0.7781 (t0) REVERT: B 76 LYS cc_start: 0.8299 (mtpt) cc_final: 0.8043 (mmmt) REVERT: P 17 LYS cc_start: 0.9001 (mmtt) cc_final: 0.8709 (mmmm) REVERT: P 101 TRP cc_start: 0.6214 (p-90) cc_final: 0.5844 (p-90) REVERT: R 21 ASN cc_start: 0.8125 (t0) cc_final: 0.7885 (t0) REVERT: R 101 TRP cc_start: 0.7031 (p-90) cc_final: 0.6813 (p-90) REVERT: T 69 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7653 (tm-30) REVERT: H 26 TYR cc_start: 0.8616 (t80) cc_final: 0.8250 (t80) REVERT: H 42 ASP cc_start: 0.8641 (t70) cc_final: 0.8134 (t70) REVERT: H 104 GLN cc_start: 0.7499 (pm20) cc_final: 0.7227 (pp30) REVERT: N 17 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8689 (mptt) REVERT: F 42 ASP cc_start: 0.8264 (t70) cc_final: 0.7539 (t70) REVERT: F 61 ASN cc_start: 0.8217 (t0) cc_final: 0.7886 (p0) REVERT: 1 17 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8838 (mmmm) REVERT: 1 21 ASN cc_start: 0.8731 (t0) cc_final: 0.8421 (t0) REVERT: 1 42 ASP cc_start: 0.8576 (t70) cc_final: 0.8321 (t0) REVERT: 1 93 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8445 (mttt) REVERT: 1 104 GLN cc_start: 0.7579 (pm20) cc_final: 0.7260 (pp30) REVERT: 3 17 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8511 (mmmm) REVERT: 3 21 ASN cc_start: 0.8961 (t0) cc_final: 0.8689 (t0) REVERT: 3 42 ASP cc_start: 0.8277 (t70) cc_final: 0.8022 (t0) REVERT: 3 93 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8722 (mmmm) REVERT: 5 17 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8305 (mmmm) REVERT: 5 21 ASN cc_start: 0.8848 (t0) cc_final: 0.8313 (t0) REVERT: 5 68 ILE cc_start: 0.8006 (mt) cc_final: 0.7772 (tp) outliers start: 70 outliers final: 58 residues processed: 635 average time/residue: 0.1331 time to fit residues: 130.9878 Evaluate side-chains 645 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 586 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 SER Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain U residue 19 ILE Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 19 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 37 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 37 SER Chi-restraints excluded: chain Y residue 19 ILE Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 19 ILE Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 29 VAL Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 37 SER Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 61 ASN Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 88 THR Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 83 VAL Chi-restraints excluded: chain 1 residue 88 THR Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 88 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 70 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 69 optimal weight: 0.6980 chunk 211 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 23 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 42 ASN 2 33 ASN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 60 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 = 0.3772 r_free = 0.3772 target = 0.113563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.090309 restraints weight = 35768.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094086 restraints weight = 19954.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096795 restraints weight = 12241.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.096510 restraints weight = 9057.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096950 restraints weight = 9562.011| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20176 Z= 0.150 Angle : 0.688 13.692 27504 Z= 0.367 Chirality : 0.043 0.189 3248 Planarity : 0.004 0.074 3520 Dihedral : 6.170 79.593 2784 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.73 % Allowed : 27.59 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.17), residues: 2576 helix: 0.96 (0.20), residues: 752 sheet: -0.19 (0.27), residues: 304 loop : -2.07 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 28 TYR 0.033 0.002 TYR Z 26 PHE 0.029 0.002 PHE N 14 TRP 0.022 0.001 TRP 5 73 Details of bonding type rmsd covalent geometry : bond 0.00343 (20176) covalent geometry : angle 0.68803 (27504) hydrogen bonds : bond 0.04327 ( 624) hydrogen bonds : angle 4.58940 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.37 seconds wall clock time: 64 minutes 55.39 seconds (3895.39 seconds total)