Starting phenix.real_space_refine on Wed Nov 20 13:50:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mks_9137/11_2024/6mks_9137.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 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 217 5.16 5 C 14508 2.51 5 N 3906 2.21 5 O 4123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 22754 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 734 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d Time building chain proxies: 4.88, per 1000 atoms: 0.21 Number of scatterers: 22754 At special positions: 0 Unit cell: (91.08, 91.08, 192.72, 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 217 16.00 O 4123 8.00 N 3906 7.00 C 14508 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: 6.58 Conformation dependent library (CDL) restraints added in 3.0 seconds 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 4.292A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 7 through 15 Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 7 through 15 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 7 through 15 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 Processing helix chain 'E' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 Processing helix chain 'F' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU G 44 " --> pdb=" O ILE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 61 Processing helix chain 'G' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 85 Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU H 44 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 61 Processing helix chain 'H' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 85 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 7 through 15 Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 61 Processing helix chain 'I' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER I 65 " --> pdb=" O LYS I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 7 through 15 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU J 44 " --> pdb=" O ILE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 61 Processing helix chain 'J' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER J 65 " --> pdb=" O LYS J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 7 through 15 Processing helix chain 'K' and resid 16 through 30 Processing helix chain 'K' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 61 Processing helix chain 'K' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER K 65 " --> pdb=" O LYS K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 7 through 15 Processing helix chain 'L' and resid 16 through 30 Processing helix chain 'L' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU L 44 " --> pdb=" O ILE L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 61 Processing helix chain 'L' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 7 through 15 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU M 44 " --> pdb=" O ILE M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 61 Processing helix chain 'M' and resid 61 through 77 removed outlier: 4.286A pdb=" N SER M 65 " --> pdb=" O LYS M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 7 through 15 Processing helix chain 'N' and resid 16 through 30 Processing helix chain 'N' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 61 Processing helix chain 'N' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER N 65 " --> pdb=" O LYS N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 85 Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 7 through 15 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU O 44 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 Processing helix chain 'O' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER O 65 " --> pdb=" O LYS O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 7 through 15 Processing helix chain 'P' and resid 16 through 30 Processing helix chain 'P' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU P 44 " --> pdb=" O ILE P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 61 Processing helix chain 'P' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER P 65 " --> pdb=" O LYS P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 7 through 15 Processing helix chain 'Q' and resid 16 through 30 Processing helix chain 'Q' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 61 Processing helix chain 'Q' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Q 65 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 85 Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 7 through 15 Processing helix chain 'R' and resid 16 through 30 Processing helix chain 'R' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 61 Processing helix chain 'R' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER R 65 " --> pdb=" O LYS R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 7 through 15 Processing helix chain 'S' and resid 16 through 30 Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU S 44 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 61 Processing helix chain 'S' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER S 65 " --> pdb=" O LYS S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 85 Processing helix chain 'T' and resid 2 through 7 Processing helix chain 'T' and resid 7 through 15 Processing helix chain 'T' and resid 16 through 30 Processing helix chain 'T' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU T 44 " --> pdb=" O ILE T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 61 Processing helix chain 'T' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER T 65 " --> pdb=" O LYS T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 85 Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 7 through 15 Processing helix chain 'U' and resid 16 through 30 Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU U 44 " --> pdb=" O ILE U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 61 Processing helix chain 'U' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER U 65 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 85 Processing helix chain 'V' and resid 2 through 7 Processing helix chain 'V' and resid 7 through 15 Processing helix chain 'V' and resid 16 through 30 Processing helix chain 'V' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU V 44 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 61 Processing helix chain 'V' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER V 65 " --> pdb=" O LYS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 85 Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 7 through 15 Processing helix chain 'W' and resid 16 through 30 Processing helix chain 'W' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU W 44 " --> pdb=" O ILE W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 61 Processing helix chain 'W' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER W 65 " --> pdb=" O LYS W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 85 Processing helix chain 'X' and resid 2 through 7 Processing helix chain 'X' and resid 7 through 15 Processing helix chain 'X' and resid 16 through 30 Processing helix chain 'X' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 61 Processing helix chain 'X' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER X 65 " --> pdb=" O LYS X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 85 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 7 through 15 Processing helix chain 'Y' and resid 16 through 30 Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Y 44 " --> pdb=" O ILE Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 Processing helix chain 'Y' and resid 61 through 77 removed outlier: 4.284A pdb=" N SER Y 65 " --> pdb=" O LYS Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 85 Processing helix chain 'Z' and resid 2 through 7 Processing helix chain 'Z' and resid 7 through 15 Processing helix chain 'Z' and resid 16 through 30 Processing helix chain 'Z' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU Z 44 " --> pdb=" O ILE Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 61 Processing helix chain 'Z' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 77 through 85 Processing helix chain 'a' and resid 2 through 7 Processing helix chain 'a' and resid 7 through 15 Processing helix chain 'a' and resid 16 through 30 Processing helix chain 'a' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU a 44 " --> pdb=" O ILE a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 61 Processing helix chain 'a' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER a 65 " --> pdb=" O LYS a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 85 Processing helix chain 'b' and resid 2 through 7 Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 16 through 30 Processing helix chain 'b' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU b 44 " --> pdb=" O ILE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 61 Processing helix chain 'b' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER b 65 " --> pdb=" O LYS b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 85 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 7 through 15 Processing helix chain 'c' and resid 16 through 30 Processing helix chain 'c' and resid 34 through 44 removed outlier: 3.871A pdb=" N GLU c 44 " --> pdb=" O ILE c 40 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 61 Processing helix chain 'c' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER c 65 " --> pdb=" O LYS c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 85 Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 7 through 15 Processing helix chain 'd' and resid 16 through 30 Processing helix chain 'd' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU d 44 " --> pdb=" O ILE d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 61 Processing helix chain 'd' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER d 65 " --> pdb=" O LYS d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 85 Processing helix chain 'e' and resid 2 through 7 Processing helix chain 'e' and resid 7 through 15 Processing helix chain 'e' and resid 16 through 30 Processing helix chain 'e' and resid 34 through 44 removed outlier: 3.870A pdb=" N GLU e 44 " --> pdb=" O ILE e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 61 Processing helix chain 'e' and resid 61 through 77 removed outlier: 4.285A pdb=" N SER e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 85 1643 hydrogen bonds defined for protein. 4929 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: 7.30 Time building geometry restraints manager: 7.40 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: 6507 1.33 - 1.45: 3463 1.45 - 1.57: 12784 1.57 - 1.69: 0 1.69 - 1.81: 341 Bond restraints: 23095 Sorted by residual: bond pdb=" CB VAL O 32 " pdb=" CG1 VAL O 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB VAL C 32 " pdb=" CG1 VAL C 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL P 32 " pdb=" CG1 VAL P 32 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.41e+00 bond pdb=" CB VAL S 32 " pdb=" CG1 VAL S 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.40e+00 bond pdb=" CB VAL N 32 " pdb=" CG1 VAL N 32 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.38e+00 ... (remaining 23090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 26522 1.27 - 2.54: 3577 2.54 - 3.80: 590 3.80 - 5.07: 280 5.07 - 6.34: 31 Bond angle restraints: 31000 Sorted by residual: angle pdb=" N GLY a 62 " pdb=" CA GLY a 62 " pdb=" C GLY a 62 " ideal model delta sigma weight residual 112.17 116.26 -4.09 1.40e+00 5.10e-01 8.51e+00 angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 112.17 116.24 -4.07 1.40e+00 5.10e-01 8.44e+00 angle pdb=" N GLY d 62 " pdb=" CA GLY d 62 " pdb=" C GLY d 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.42e+00 angle pdb=" N GLY Q 62 " pdb=" CA GLY Q 62 " pdb=" C GLY Q 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.40e+00 angle pdb=" N GLY D 62 " pdb=" CA GLY D 62 " pdb=" C GLY D 62 " ideal model delta sigma weight residual 112.17 116.23 -4.06 1.40e+00 5.10e-01 8.39e+00 ... (remaining 30995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.40: 13500 14.40 - 28.81: 433 28.81 - 43.21: 141 43.21 - 57.62: 0 57.62 - 72.02: 31 Dihedral angle restraints: 14105 sinusoidal: 5983 harmonic: 8122 Sorted by residual: dihedral pdb=" C GLU V 64 " pdb=" N GLU V 64 " pdb=" CA GLU V 64 " pdb=" CB GLU V 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Y 64 " pdb=" N GLU Y 64 " pdb=" CA GLU Y 64 " pdb=" CB GLU Y 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C GLU Z 64 " pdb=" N GLU Z 64 " pdb=" CA GLU Z 64 " pdb=" CB GLU Z 64 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 14102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2690 0.071 - 0.142: 689 0.142 - 0.212: 58 0.212 - 0.283: 4 0.283 - 0.354: 31 Chirality restraints: 3472 Sorted by residual: chirality pdb=" CA GLU Y 64 " pdb=" N GLU Y 64 " pdb=" C GLU Y 64 " pdb=" CB GLU Y 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA GLU V 64 " pdb=" N GLU V 64 " pdb=" C GLU V 64 " pdb=" CB GLU V 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA GLU O 64 " pdb=" N GLU O 64 " pdb=" C GLU O 64 " pdb=" CB GLU O 64 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 3469 not shown) Planarity restraints: 3937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 53 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.38e+00 pdb=" C GLY Q 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY Q 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE Q 54 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 53 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" C GLY b 53 " 0.020 2.00e-02 2.50e+03 pdb=" O GLY b 53 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE b 54 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 53 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C GLY J 53 " -0.020 2.00e-02 2.50e+03 pdb=" O GLY J 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE J 54 " 0.007 2.00e-02 2.50e+03 ... (remaining 3934 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 7884 2.87 - 3.38: 26030 3.38 - 3.89: 40131 3.89 - 4.39: 46241 4.39 - 4.90: 77147 Nonbonded interactions: 197433 Sorted by model distance: nonbonded pdb=" OD2 ASP d 26 " pdb=" NE1 TRP d 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP P 26 " pdb=" NE1 TRP P 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP W 26 " pdb=" NE1 TRP W 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP X 26 " pdb=" NE1 TRP X 76 " model vdw 2.367 3.120 nonbonded pdb=" OD2 ASP T 26 " pdb=" NE1 TRP T 76 " model vdw 2.367 3.120 ... (remaining 197428 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 41.420 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.012 0.084 23095 Z= 0.763 Angle : 1.000 6.341 31000 Z= 0.560 Chirality : 0.067 0.354 3472 Planarity : 0.004 0.012 3937 Dihedral : 9.700 72.020 8773 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2728 helix: -0.59 (0.09), residues: 2449 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 30 HIS 0.002 0.001 HIS O 56 PHE 0.009 0.003 PHE N 3 TYR 0.006 0.002 TYR e 78 ARG 0.001 0.000 ARG M 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1755 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7149 (ttm170) REVERT: A 66 CYS cc_start: 0.8627 (m) cc_final: 0.8309 (m) REVERT: A 76 TRP cc_start: 0.8492 (m100) cc_final: 0.7794 (m100) REVERT: B 6 ASP cc_start: 0.8289 (m-30) cc_final: 0.8057 (m-30) REVERT: B 17 MET cc_start: 0.8125 (tpp) cc_final: 0.7760 (tpt) REVERT: B 19 VAL cc_start: 0.9206 (t) cc_final: 0.8977 (t) REVERT: B 33 LEU cc_start: 0.9004 (mt) cc_final: 0.8672 (mt) REVERT: B 34 ASN cc_start: 0.7590 (t160) cc_final: 0.6870 (t0) REVERT: B 66 CYS cc_start: 0.8602 (m) cc_final: 0.8352 (m) REVERT: B 83 ASP cc_start: 0.8552 (t70) cc_final: 0.8312 (t0) REVERT: C 3 PHE cc_start: 0.8737 (t80) cc_final: 0.8497 (t80) REVERT: C 19 VAL cc_start: 0.9339 (t) cc_final: 0.9132 (t) REVERT: C 39 ASN cc_start: 0.7774 (m-40) cc_final: 0.7529 (m110) REVERT: C 60 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8146 (mtpp) REVERT: C 83 ASP cc_start: 0.8575 (t70) cc_final: 0.8355 (t70) REVERT: D 13 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8736 (mm-40) REVERT: D 35 ARG cc_start: 0.7260 (ttm110) cc_final: 0.6856 (tpp80) REVERT: D 39 ASN cc_start: 0.7737 (m-40) cc_final: 0.7305 (m110) REVERT: D 43 CYS cc_start: 0.7877 (p) cc_final: 0.7051 (p) REVERT: D 66 CYS cc_start: 0.8461 (m) cc_final: 0.8236 (m) REVERT: D 74 LYS cc_start: 0.8662 (tttt) cc_final: 0.8416 (ttpp) REVERT: D 76 TRP cc_start: 0.8347 (m100) cc_final: 0.8099 (m100) REVERT: D 87 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7790 (mm110) REVERT: E 13 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8889 (mm110) REVERT: E 17 MET cc_start: 0.8091 (tpp) cc_final: 0.7822 (tpt) REVERT: E 40 ILE cc_start: 0.8708 (mt) cc_final: 0.8496 (pt) REVERT: E 82 GLN cc_start: 0.8825 (mm110) cc_final: 0.8613 (mm110) REVERT: F 19 VAL cc_start: 0.9248 (t) cc_final: 0.8873 (t) REVERT: F 34 ASN cc_start: 0.7392 (t160) cc_final: 0.7128 (t160) REVERT: F 40 ILE cc_start: 0.8870 (mt) cc_final: 0.8649 (pt) REVERT: F 66 CYS cc_start: 0.8736 (m) cc_final: 0.8385 (m) REVERT: F 82 GLN cc_start: 0.8569 (mm110) cc_final: 0.7968 (mm110) REVERT: G 18 THR cc_start: 0.8815 (p) cc_final: 0.8583 (p) REVERT: G 33 LEU cc_start: 0.9030 (mt) cc_final: 0.8803 (mt) REVERT: G 34 ASN cc_start: 0.7192 (t160) cc_final: 0.6204 (t0) REVERT: G 35 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6622 (tpp80) REVERT: G 39 ASN cc_start: 0.7809 (m-40) cc_final: 0.7554 (m110) REVERT: G 48 GLN cc_start: 0.8393 (mp10) cc_final: 0.7722 (mp10) REVERT: G 83 ASP cc_start: 0.8527 (t70) cc_final: 0.8307 (t0) REVERT: H 3 PHE cc_start: 0.8631 (t80) cc_final: 0.8377 (t80) REVERT: H 17 MET cc_start: 0.8015 (tpp) cc_final: 0.7804 (tpt) REVERT: H 31 ASN cc_start: 0.9165 (m-40) cc_final: 0.8914 (m-40) REVERT: H 76 TRP cc_start: 0.8425 (m100) cc_final: 0.7876 (m100) REVERT: H 87 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7862 (mm110) REVERT: I 13 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8764 (mm-40) REVERT: I 17 MET cc_start: 0.8192 (tpp) cc_final: 0.7981 (tpt) REVERT: I 34 ASN cc_start: 0.7683 (t160) cc_final: 0.7064 (t160) REVERT: I 76 TRP cc_start: 0.8322 (m100) cc_final: 0.7599 (m100) REVERT: J 5 LYS cc_start: 0.8554 (tttm) cc_final: 0.8336 (tttt) REVERT: J 8 SER cc_start: 0.8929 (p) cc_final: 0.8690 (p) REVERT: J 12 ILE cc_start: 0.9483 (mt) cc_final: 0.9205 (mp) REVERT: J 17 MET cc_start: 0.8444 (tpp) cc_final: 0.8165 (tpp) REVERT: J 19 VAL cc_start: 0.9363 (t) cc_final: 0.9128 (t) REVERT: J 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6793 (tpp80) REVERT: J 39 ASN cc_start: 0.8096 (m-40) cc_final: 0.7712 (m-40) REVERT: J 48 GLN cc_start: 0.8529 (mp10) cc_final: 0.8322 (mp10) REVERT: J 76 TRP cc_start: 0.8486 (m100) cc_final: 0.8046 (m100) REVERT: K 3 PHE cc_start: 0.8709 (t80) cc_final: 0.8398 (t80) REVERT: K 13 GLN cc_start: 0.9090 (mm-40) cc_final: 0.7750 (mm-40) REVERT: K 21 LYS cc_start: 0.8668 (mttt) cc_final: 0.8440 (mttp) REVERT: K 25 ASP cc_start: 0.8103 (m-30) cc_final: 0.7193 (m-30) REVERT: K 39 ASN cc_start: 0.8117 (m-40) cc_final: 0.7846 (m110) REVERT: K 60 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7921 (mtpt) REVERT: K 66 CYS cc_start: 0.8537 (m) cc_final: 0.8213 (m) REVERT: K 83 ASP cc_start: 0.8615 (t70) cc_final: 0.8101 (t0) REVERT: K 87 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7075 (mm110) REVERT: L 6 ASP cc_start: 0.8341 (m-30) cc_final: 0.8083 (m-30) REVERT: L 35 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6886 (ttm-80) REVERT: L 66 CYS cc_start: 0.8336 (m) cc_final: 0.7957 (m) REVERT: L 87 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7645 (mm110) REVERT: M 13 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8075 (mm-40) REVERT: M 39 ASN cc_start: 0.8025 (m-40) cc_final: 0.7424 (m110) REVERT: M 77 ASN cc_start: 0.9238 (t0) cc_final: 0.9025 (t0) REVERT: N 39 ASN cc_start: 0.7782 (m-40) cc_final: 0.7452 (m110) REVERT: O 6 ASP cc_start: 0.8362 (m-30) cc_final: 0.8156 (m-30) REVERT: O 34 ASN cc_start: 0.7612 (t160) cc_final: 0.6626 (t0) REVERT: O 35 ARG cc_start: 0.7268 (ttm110) cc_final: 0.6819 (ttp-110) REVERT: O 39 ASN cc_start: 0.7849 (m-40) cc_final: 0.7531 (m110) REVERT: O 48 GLN cc_start: 0.8435 (mp10) cc_final: 0.7974 (mp10) REVERT: O 61 LYS cc_start: 0.8895 (mttm) cc_final: 0.8649 (mttm) REVERT: P 12 ILE cc_start: 0.9366 (mt) cc_final: 0.9077 (mm) REVERT: P 13 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8037 (mm110) REVERT: P 66 CYS cc_start: 0.8584 (m) cc_final: 0.8186 (m) REVERT: P 67 ASN cc_start: 0.8777 (m-40) cc_final: 0.8435 (m-40) REVERT: Q 82 GLN cc_start: 0.8454 (mm110) cc_final: 0.8215 (mm-40) REVERT: R 5 LYS cc_start: 0.8713 (tttm) cc_final: 0.8498 (tttt) REVERT: R 8 SER cc_start: 0.9050 (p) cc_final: 0.8809 (p) REVERT: R 13 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8741 (mm110) REVERT: R 32 VAL cc_start: 0.9186 (m) cc_final: 0.8944 (p) REVERT: R 35 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6712 (tpp80) REVERT: R 39 ASN cc_start: 0.7893 (m-40) cc_final: 0.7046 (m-40) REVERT: R 61 LYS cc_start: 0.9090 (mttm) cc_final: 0.8438 (mttm) REVERT: R 70 LEU cc_start: 0.9300 (mt) cc_final: 0.9031 (mt) REVERT: R 77 ASN cc_start: 0.9263 (t0) cc_final: 0.8702 (t0) REVERT: S 3 PHE cc_start: 0.8259 (t80) cc_final: 0.7801 (t80) REVERT: S 19 VAL cc_start: 0.9229 (t) cc_final: 0.8945 (t) REVERT: S 39 ASN cc_start: 0.7746 (m-40) cc_final: 0.7490 (m110) REVERT: S 48 GLN cc_start: 0.8310 (mp10) cc_final: 0.8074 (mp10) REVERT: S 60 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8290 (mtpt) REVERT: S 66 CYS cc_start: 0.8570 (m) cc_final: 0.8059 (m) REVERT: T 13 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8886 (mm110) REVERT: T 17 MET cc_start: 0.8062 (tpp) cc_final: 0.7829 (tpp) REVERT: T 34 ASN cc_start: 0.7742 (t160) cc_final: 0.7077 (t0) REVERT: T 35 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6695 (ttm-80) REVERT: T 39 ASN cc_start: 0.7794 (m-40) cc_final: 0.7362 (m110) REVERT: T 82 GLN cc_start: 0.8502 (mm110) cc_final: 0.8276 (mm110) REVERT: T 83 ASP cc_start: 0.8645 (t70) cc_final: 0.8274 (t70) REVERT: U 25 ASP cc_start: 0.8325 (m-30) cc_final: 0.7892 (m-30) REVERT: U 26 ASP cc_start: 0.8090 (m-30) cc_final: 0.7883 (m-30) REVERT: U 35 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6650 (ttm-80) REVERT: U 39 ASN cc_start: 0.7550 (m-40) cc_final: 0.7321 (m110) REVERT: U 49 ASP cc_start: 0.8515 (m-30) cc_final: 0.8286 (m-30) REVERT: V 35 ARG cc_start: 0.7359 (ttm110) cc_final: 0.6840 (ttm110) REVERT: V 39 ASN cc_start: 0.7947 (m-40) cc_final: 0.7611 (m-40) REVERT: V 66 CYS cc_start: 0.8665 (m) cc_final: 0.8362 (m) REVERT: V 87 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7437 (mm110) REVERT: W 4 ILE cc_start: 0.8915 (mt) cc_final: 0.8508 (mt) REVERT: W 6 ASP cc_start: 0.8376 (m-30) cc_final: 0.8116 (m-30) REVERT: W 12 ILE cc_start: 0.9419 (mt) cc_final: 0.9201 (mt) REVERT: W 17 MET cc_start: 0.7951 (tpp) cc_final: 0.7622 (tpt) REVERT: W 33 LEU cc_start: 0.9068 (mt) cc_final: 0.8826 (mt) REVERT: W 34 ASN cc_start: 0.7543 (t160) cc_final: 0.6678 (t0) REVERT: W 66 CYS cc_start: 0.8650 (m) cc_final: 0.8428 (t) REVERT: W 76 TRP cc_start: 0.8384 (m100) cc_final: 0.8069 (m100) REVERT: X 3 PHE cc_start: 0.8879 (t80) cc_final: 0.8651 (t80) REVERT: X 25 ASP cc_start: 0.8313 (m-30) cc_final: 0.7969 (m-30) REVERT: X 48 GLN cc_start: 0.8459 (mp10) cc_final: 0.8151 (mp10) REVERT: X 66 CYS cc_start: 0.8844 (m) cc_final: 0.8280 (m) REVERT: X 82 GLN cc_start: 0.8532 (mm110) cc_final: 0.8301 (mm110) REVERT: X 87 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7476 (mm-40) REVERT: Y 5 LYS cc_start: 0.8416 (tttm) cc_final: 0.8210 (tttt) REVERT: Y 13 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8787 (mm110) REVERT: Y 17 MET cc_start: 0.8083 (tpp) cc_final: 0.7830 (tpt) REVERT: Y 19 VAL cc_start: 0.9410 (t) cc_final: 0.9113 (t) REVERT: Y 25 ASP cc_start: 0.8163 (m-30) cc_final: 0.7760 (m-30) REVERT: Y 35 ARG cc_start: 0.7409 (ttm110) cc_final: 0.7120 (ttp-110) REVERT: Y 39 ASN cc_start: 0.7715 (m-40) cc_final: 0.7346 (m-40) REVERT: Y 55 ILE cc_start: 0.9135 (mt) cc_final: 0.8823 (tt) REVERT: Y 60 LYS cc_start: 0.8991 (mtmt) cc_final: 0.7724 (tptt) REVERT: Y 61 LYS cc_start: 0.8678 (mttm) cc_final: 0.8400 (mttt) REVERT: Y 66 CYS cc_start: 0.8484 (m) cc_final: 0.8025 (m) REVERT: Z 8 SER cc_start: 0.8825 (p) cc_final: 0.8576 (p) REVERT: Z 12 ILE cc_start: 0.9465 (mt) cc_final: 0.9091 (mp) REVERT: Z 17 MET cc_start: 0.7915 (tpp) cc_final: 0.7487 (tpt) REVERT: Z 34 ASN cc_start: 0.7797 (t160) cc_final: 0.7035 (t0) REVERT: Z 36 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6801 (mt-10) REVERT: Z 48 GLN cc_start: 0.8487 (mp10) cc_final: 0.8174 (mp10) REVERT: Z 66 CYS cc_start: 0.8490 (m) cc_final: 0.8131 (m) REVERT: Z 77 ASN cc_start: 0.8985 (t0) cc_final: 0.8457 (t0) REVERT: a 3 PHE cc_start: 0.8669 (t80) cc_final: 0.8395 (t80) REVERT: a 5 LYS cc_start: 0.8766 (tttm) cc_final: 0.8364 (tptt) REVERT: a 8 SER cc_start: 0.9250 (p) cc_final: 0.8908 (p) REVERT: a 9 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7476 (mmt-90) REVERT: a 12 ILE cc_start: 0.9346 (mt) cc_final: 0.9009 (mp) REVERT: a 27 LEU cc_start: 0.8787 (mt) cc_final: 0.8489 (mt) REVERT: a 31 ASN cc_start: 0.9112 (m-40) cc_final: 0.8889 (m-40) REVERT: a 34 ASN cc_start: 0.7737 (t160) cc_final: 0.7168 (t0) REVERT: a 35 ARG cc_start: 0.7538 (ttm110) cc_final: 0.7129 (ttm-80) REVERT: a 39 ASN cc_start: 0.8156 (m-40) cc_final: 0.7898 (m110) REVERT: a 83 ASP cc_start: 0.8536 (t70) cc_final: 0.8328 (t0) REVERT: a 87 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7303 (mm-40) REVERT: b 3 PHE cc_start: 0.8633 (t80) cc_final: 0.8432 (t80) REVERT: b 23 ILE cc_start: 0.8821 (mt) cc_final: 0.8616 (mt) REVERT: b 36 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6742 (mt-10) REVERT: b 39 ASN cc_start: 0.7840 (m-40) cc_final: 0.7515 (m110) REVERT: b 49 ASP cc_start: 0.8403 (m-30) cc_final: 0.8173 (m-30) REVERT: b 66 CYS cc_start: 0.8568 (m) cc_final: 0.8353 (m) REVERT: c 17 MET cc_start: 0.8383 (tpp) cc_final: 0.8153 (tpt) REVERT: c 19 VAL cc_start: 0.9349 (t) cc_final: 0.8973 (t) REVERT: c 35 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7290 (tpp80) REVERT: c 39 ASN cc_start: 0.7626 (m-40) cc_final: 0.6958 (m110) REVERT: c 74 LYS cc_start: 0.8614 (tttt) cc_final: 0.8397 (ttpp) REVERT: c 82 GLN cc_start: 0.8925 (mm110) cc_final: 0.8489 (mm110) REVERT: c 87 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7050 (mm110) REVERT: d 3 PHE cc_start: 0.8733 (t80) cc_final: 0.8530 (t80) REVERT: d 13 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8501 (mm110) REVERT: d 33 LEU cc_start: 0.9052 (mt) cc_final: 0.8731 (mt) REVERT: d 40 ILE cc_start: 0.8699 (mt) cc_final: 0.8439 (pt) REVERT: d 66 CYS cc_start: 0.8666 (m) cc_final: 0.8421 (m) REVERT: d 82 GLN cc_start: 0.8888 (mm110) cc_final: 0.8672 (mm-40) REVERT: d 83 ASP cc_start: 0.8460 (t70) cc_final: 0.8239 (t0) REVERT: e 34 ASN cc_start: 0.7798 (t160) cc_final: 0.7392 (t0) REVERT: e 35 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6651 (tpp80) REVERT: e 39 ASN cc_start: 0.7689 (m-40) cc_final: 0.6498 (m110) REVERT: e 70 LEU cc_start: 0.8976 (mt) cc_final: 0.8720 (mt) REVERT: e 74 LYS cc_start: 0.8709 (tttt) cc_final: 0.8457 (ttpp) REVERT: e 87 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8409 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1755 average time/residue: 0.3811 time to fit residues: 1003.6906 Evaluate side-chains 1502 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1502 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 39 ASN A 67 ASN A 82 GLN B 13 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN B 67 ASN B 82 GLN C 31 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 56 HIS D 82 GLN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 56 HIS E 67 ASN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 34 ASN G 39 ASN G 67 ASN G 82 GLN H 13 GLN H 67 ASN H 82 GLN I 13 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 HIS I 82 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 ASN J 56 HIS J 67 ASN J 82 GLN K 31 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN K 56 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN L 56 HIS L 67 ASN L 82 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 ASN M 56 HIS ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 ASN N 56 HIS N 67 ASN N 82 GLN O 13 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 ASN O 56 HIS O 67 ASN O 82 GLN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 HIS P 82 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 HIS R 82 GLN ** S 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 56 HIS S 82 GLN ** T 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 ASN T 56 HIS ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 56 HIS U 67 ASN U 82 GLN ** V 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 HIS V 82 GLN W 13 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS W 67 ASN W 82 GLN X 67 ASN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 ASN Y 67 ASN Y 82 GLN ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 56 HIS Z 67 ASN Z 82 GLN ** a 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN a 39 ASN a 82 GLN b 39 ASN b 56 HIS ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 56 HIS d 67 ASN e 34 ASN e 67 ASN Total number of N/Q/H flips: 83 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23095 Z= 0.254 Angle : 0.572 5.745 31000 Z= 0.316 Chirality : 0.042 0.206 3472 Planarity : 0.004 0.042 3937 Dihedral : 4.043 14.909 2914 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.70 % Allowed : 14.54 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 2728 helix: 0.94 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -1.80 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 76 HIS 0.005 0.001 HIS G 56 PHE 0.022 0.002 PHE I 28 TYR 0.007 0.002 TYR b 78 ARG 0.007 0.001 ARG P 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 1712 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6841 (tpp) cc_final: 0.6597 (tpp) REVERT: A 9 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.7873 (ttp-110) REVERT: A 22 GLN cc_start: 0.8495 (mt0) cc_final: 0.8100 (mt0) REVERT: A 34 ASN cc_start: 0.7925 (t0) cc_final: 0.6908 (t0) REVERT: A 47 GLU cc_start: 0.7288 (tt0) cc_final: 0.6779 (tt0) REVERT: A 66 CYS cc_start: 0.8659 (m) cc_final: 0.8228 (m) REVERT: A 71 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9074 (ttpp) REVERT: B 35 ARG cc_start: 0.7790 (ttm110) cc_final: 0.7579 (ttp-110) REVERT: B 52 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7701 (mtt-85) REVERT: B 60 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8561 (mtmm) REVERT: B 66 CYS cc_start: 0.8406 (m) cc_final: 0.8188 (m) REVERT: B 74 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8675 (ptmm) REVERT: B 83 ASP cc_start: 0.8592 (t70) cc_final: 0.8365 (t0) REVERT: C 2 ASN cc_start: 0.7687 (m-40) cc_final: 0.7040 (m-40) REVERT: C 22 GLN cc_start: 0.8531 (mt0) cc_final: 0.8256 (mt0) REVERT: C 35 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7283 (ttm110) REVERT: C 60 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8437 (mtpp) REVERT: C 78 TYR cc_start: 0.8891 (t80) cc_final: 0.8681 (t80) REVERT: C 83 ASP cc_start: 0.8587 (t70) cc_final: 0.8275 (t0) REVERT: D 13 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8822 (mm-40) REVERT: D 39 ASN cc_start: 0.8171 (m110) cc_final: 0.7617 (m-40) REVERT: D 60 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8375 (mtpp) REVERT: D 74 LYS cc_start: 0.8777 (tttt) cc_final: 0.8499 (ttpp) REVERT: D 77 ASN cc_start: 0.9148 (t0) cc_final: 0.8912 (t0) REVERT: D 78 TYR cc_start: 0.8719 (t80) cc_final: 0.8314 (t80) REVERT: E 1 MET cc_start: 0.6830 (tpp) cc_final: 0.6512 (tpt) REVERT: E 57 MET cc_start: 0.8028 (mtm) cc_final: 0.7712 (mtp) REVERT: E 60 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8478 (mtpp) REVERT: E 82 GLN cc_start: 0.8751 (mm110) cc_final: 0.8364 (mm110) REVERT: F 2 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7548 (m-40) REVERT: F 6 ASP cc_start: 0.8226 (m-30) cc_final: 0.7932 (p0) REVERT: F 82 GLN cc_start: 0.8633 (mm110) cc_final: 0.8431 (mm110) REVERT: F 87 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7713 (mm110) REVERT: G 35 ARG cc_start: 0.7602 (ttm110) cc_final: 0.7348 (ttp-110) REVERT: G 39 ASN cc_start: 0.8330 (m110) cc_final: 0.7982 (m110) REVERT: G 67 ASN cc_start: 0.8830 (m-40) cc_final: 0.8589 (m110) REVERT: G 76 TRP cc_start: 0.8868 (m100) cc_final: 0.8608 (m100) REVERT: G 77 ASN cc_start: 0.9065 (t0) cc_final: 0.8746 (t0) REVERT: G 83 ASP cc_start: 0.8459 (t70) cc_final: 0.8204 (t0) REVERT: H 2 ASN cc_start: 0.7479 (m-40) cc_final: 0.7131 (m110) REVERT: H 6 ASP cc_start: 0.8114 (m-30) cc_final: 0.7898 (m-30) REVERT: H 7 ASN cc_start: 0.8798 (m-40) cc_final: 0.8430 (m110) REVERT: H 9 ARG cc_start: 0.8709 (mtp-110) cc_final: 0.8502 (mtp-110) REVERT: H 21 LYS cc_start: 0.8830 (mttt) cc_final: 0.8571 (mttp) REVERT: H 31 ASN cc_start: 0.9157 (m-40) cc_final: 0.8931 (m-40) REVERT: H 34 ASN cc_start: 0.7620 (t0) cc_final: 0.6627 (t0) REVERT: H 60 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8259 (mtpt) REVERT: I 7 ASN cc_start: 0.8910 (m-40) cc_final: 0.8684 (m110) REVERT: I 9 ARG cc_start: 0.8487 (mtp-110) cc_final: 0.8222 (mtp-110) REVERT: I 49 ASP cc_start: 0.8573 (m-30) cc_final: 0.8337 (m-30) REVERT: J 34 ASN cc_start: 0.7991 (t0) cc_final: 0.7318 (t0) REVERT: J 39 ASN cc_start: 0.8434 (m110) cc_final: 0.8081 (m110) REVERT: J 60 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8321 (mttt) REVERT: J 71 LYS cc_start: 0.9267 (ttmt) cc_final: 0.9057 (ttmm) REVERT: J 77 ASN cc_start: 0.9135 (t0) cc_final: 0.8786 (t0) REVERT: K 21 LYS cc_start: 0.9012 (mttt) cc_final: 0.8640 (mttp) REVERT: K 25 ASP cc_start: 0.8052 (m-30) cc_final: 0.7586 (m-30) REVERT: K 33 LEU cc_start: 0.8938 (mp) cc_final: 0.8575 (mp) REVERT: K 34 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.6452 (t0) REVERT: K 60 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8121 (mtpp) REVERT: K 66 CYS cc_start: 0.8552 (m) cc_final: 0.8343 (m) REVERT: K 78 TYR cc_start: 0.8949 (t80) cc_final: 0.8641 (t80) REVERT: K 83 ASP cc_start: 0.8707 (t70) cc_final: 0.8315 (t0) REVERT: L 6 ASP cc_start: 0.8278 (m-30) cc_final: 0.8067 (m-30) REVERT: L 21 LYS cc_start: 0.9293 (mttp) cc_final: 0.8962 (mttm) REVERT: L 26 ASP cc_start: 0.8442 (m-30) cc_final: 0.8160 (m-30) REVERT: L 35 ARG cc_start: 0.7656 (ttm110) cc_final: 0.6800 (tpp80) REVERT: L 37 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7752 (mt-10) REVERT: M 39 ASN cc_start: 0.8506 (m110) cc_final: 0.8053 (m-40) REVERT: M 52 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7702 (mtt-85) REVERT: M 60 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8318 (mtpt) REVERT: N 1 MET cc_start: 0.6389 (tpt) cc_final: 0.6042 (tpp) REVERT: N 2 ASN cc_start: 0.8371 (m-40) cc_final: 0.7924 (m110) REVERT: N 20 ILE cc_start: 0.9195 (mt) cc_final: 0.8956 (mp) REVERT: N 34 ASN cc_start: 0.7867 (t160) cc_final: 0.6701 (t0) REVERT: N 35 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7180 (ttp-110) REVERT: N 37 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7934 (mp0) REVERT: N 60 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8114 (mtpp) REVERT: N 66 CYS cc_start: 0.8635 (m) cc_final: 0.8201 (m) REVERT: N 78 TYR cc_start: 0.8869 (t80) cc_final: 0.8543 (t80) REVERT: N 82 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8281 (mm110) REVERT: N 89 LEU cc_start: 0.6805 (tp) cc_final: 0.6436 (tp) REVERT: O 2 ASN cc_start: 0.8117 (m-40) cc_final: 0.7522 (m-40) REVERT: O 35 ARG cc_start: 0.7545 (ttm110) cc_final: 0.6975 (tpp80) REVERT: O 39 ASN cc_start: 0.8335 (m110) cc_final: 0.7651 (m110) REVERT: O 44 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7555 (mm-30) REVERT: O 60 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8326 (mtpt) REVERT: P 2 ASN cc_start: 0.7309 (m-40) cc_final: 0.7106 (m-40) REVERT: P 25 ASP cc_start: 0.8127 (m-30) cc_final: 0.7881 (m-30) REVERT: P 33 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9021 (tp) REVERT: P 34 ASN cc_start: 0.7768 (t160) cc_final: 0.7276 (t0) REVERT: P 60 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8659 (mtpt) REVERT: P 66 CYS cc_start: 0.8695 (m) cc_final: 0.8259 (m) REVERT: P 67 ASN cc_start: 0.8923 (m-40) cc_final: 0.8538 (m-40) REVERT: Q 7 ASN cc_start: 0.8620 (m-40) cc_final: 0.8070 (m110) REVERT: Q 34 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7287 (t0) REVERT: Q 60 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8774 (mtpt) REVERT: Q 66 CYS cc_start: 0.8490 (m) cc_final: 0.7959 (m) REVERT: R 1 MET cc_start: 0.7098 (tpp) cc_final: 0.6792 (tpp) REVERT: R 21 LYS cc_start: 0.9260 (mttt) cc_final: 0.8738 (mttt) REVERT: R 35 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7330 (tpp80) REVERT: R 36 GLU cc_start: 0.7010 (mp0) cc_final: 0.6495 (mp0) REVERT: R 57 MET cc_start: 0.7965 (mtt) cc_final: 0.7533 (mtp) REVERT: R 60 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8333 (mttt) REVERT: R 66 CYS cc_start: 0.8426 (m) cc_final: 0.8075 (m) REVERT: S 34 ASN cc_start: 0.8005 (t0) cc_final: 0.7169 (t0) REVERT: S 39 ASN cc_start: 0.8394 (m-40) cc_final: 0.8106 (m110) REVERT: S 56 HIS cc_start: 0.8172 (m90) cc_final: 0.7576 (m-70) REVERT: S 60 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8620 (mtpt) REVERT: S 66 CYS cc_start: 0.8696 (m) cc_final: 0.8354 (m) REVERT: S 78 TYR cc_start: 0.8878 (t80) cc_final: 0.8545 (t80) REVERT: S 82 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8433 (mm110) REVERT: T 21 LYS cc_start: 0.9186 (mttp) cc_final: 0.8971 (mttm) REVERT: T 35 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7313 (ttp-110) REVERT: T 39 ASN cc_start: 0.8260 (m110) cc_final: 0.7589 (m110) REVERT: T 83 ASP cc_start: 0.8721 (t70) cc_final: 0.8451 (t70) REVERT: U 2 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7623 (m-40) REVERT: U 34 ASN cc_start: 0.8224 (t0) cc_final: 0.7600 (t0) REVERT: U 35 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7209 (ttp-110) REVERT: U 39 ASN cc_start: 0.8143 (m110) cc_final: 0.7520 (m110) REVERT: U 47 GLU cc_start: 0.7655 (tt0) cc_final: 0.6963 (tt0) REVERT: U 49 ASP cc_start: 0.8522 (m-30) cc_final: 0.8233 (m-30) REVERT: U 60 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8408 (mtpp) REVERT: V 34 ASN cc_start: 0.7843 (t0) cc_final: 0.7425 (t0) REVERT: V 39 ASN cc_start: 0.8391 (m-40) cc_final: 0.8051 (m110) REVERT: V 66 CYS cc_start: 0.8660 (m) cc_final: 0.8337 (m) REVERT: W 6 ASP cc_start: 0.8345 (m-30) cc_final: 0.8091 (m-30) REVERT: W 35 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7410 (ttp-110) REVERT: W 39 ASN cc_start: 0.8095 (m-40) cc_final: 0.7379 (m110) REVERT: W 47 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: X 21 LYS cc_start: 0.9064 (mttp) cc_final: 0.8247 (mttp) REVERT: X 25 ASP cc_start: 0.8132 (m-30) cc_final: 0.7706 (m-30) REVERT: X 39 ASN cc_start: 0.8450 (m110) cc_final: 0.8107 (m-40) REVERT: X 60 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8464 (mtpt) REVERT: X 66 CYS cc_start: 0.8715 (m) cc_final: 0.8036 (m) REVERT: Y 21 LYS cc_start: 0.9061 (mttp) cc_final: 0.8757 (mttm) REVERT: Y 25 ASP cc_start: 0.8402 (m-30) cc_final: 0.7643 (m-30) REVERT: Y 60 LYS cc_start: 0.9147 (mtmt) cc_final: 0.7929 (tptt) REVERT: Y 66 CYS cc_start: 0.8338 (m) cc_final: 0.7957 (m) REVERT: Z 2 ASN cc_start: 0.7937 (m-40) cc_final: 0.7575 (m110) REVERT: Z 9 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7747 (mtp85) REVERT: Z 13 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8183 (mm-40) REVERT: Z 18 THR cc_start: 0.9300 (m) cc_final: 0.9089 (p) REVERT: Z 34 ASN cc_start: 0.8042 (t160) cc_final: 0.7596 (m-40) REVERT: Z 37 GLU cc_start: 0.8129 (mt-10) cc_final: 0.6848 (mt-10) REVERT: Z 44 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7670 (mm-30) REVERT: Z 60 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8332 (mtpt) REVERT: Z 61 LYS cc_start: 0.8702 (mttp) cc_final: 0.8393 (mttm) REVERT: Z 77 ASN cc_start: 0.8910 (t0) cc_final: 0.8229 (t0) REVERT: a 2 ASN cc_start: 0.7893 (m-40) cc_final: 0.7560 (m110) REVERT: a 5 LYS cc_start: 0.8783 (tttm) cc_final: 0.8141 (tptt) REVERT: a 8 SER cc_start: 0.9148 (p) cc_final: 0.8831 (m) REVERT: a 9 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7455 (mmt-90) REVERT: a 35 ARG cc_start: 0.7373 (ttm110) cc_final: 0.7075 (ttm110) REVERT: a 36 GLU cc_start: 0.7937 (mp0) cc_final: 0.7698 (mp0) REVERT: a 45 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7701 (tttp) REVERT: a 60 LYS cc_start: 0.8974 (mtmt) cc_final: 0.7645 (tptm) REVERT: b 22 GLN cc_start: 0.8996 (mt0) cc_final: 0.8779 (mt0) REVERT: b 37 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7669 (mt-10) REVERT: b 39 ASN cc_start: 0.8066 (m110) cc_final: 0.7626 (m110) REVERT: b 57 MET cc_start: 0.8262 (mtp) cc_final: 0.8012 (mtp) REVERT: b 58 ILE cc_start: 0.8985 (tp) cc_final: 0.8727 (tp) REVERT: b 71 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9184 (ttpp) REVERT: b 74 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8904 (ttmm) REVERT: b 77 ASN cc_start: 0.9027 (t0) cc_final: 0.8731 (t0) REVERT: c 20 ILE cc_start: 0.9110 (mt) cc_final: 0.8847 (mp) REVERT: c 35 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7469 (tpp80) REVERT: c 39 ASN cc_start: 0.8464 (m-40) cc_final: 0.7696 (m110) REVERT: c 44 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7777 (mm-30) REVERT: c 47 GLU cc_start: 0.7659 (tt0) cc_final: 0.7448 (tt0) REVERT: c 48 GLN cc_start: 0.8417 (mp10) cc_final: 0.7839 (mp10) REVERT: c 58 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8980 (tp) REVERT: d 1 MET cc_start: 0.7322 (tpp) cc_final: 0.6924 (tpt) REVERT: d 2 ASN cc_start: 0.8088 (m-40) cc_final: 0.7866 (m-40) REVERT: d 3 PHE cc_start: 0.8873 (t80) cc_final: 0.8624 (t80) REVERT: d 13 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8745 (mm110) REVERT: d 34 ASN cc_start: 0.7795 (t160) cc_final: 0.7124 (p0) REVERT: d 60 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8337 (mtpp) REVERT: d 74 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8883 (ttpp) REVERT: d 82 GLN cc_start: 0.9023 (mm110) cc_final: 0.8797 (mm-40) REVERT: d 83 ASP cc_start: 0.8574 (t70) cc_final: 0.8275 (t0) REVERT: e 13 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8768 (mm-40) REVERT: e 34 ASN cc_start: 0.8126 (t0) cc_final: 0.7659 (t0) REVERT: e 35 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7116 (ttp-110) REVERT: e 39 ASN cc_start: 0.8369 (m-40) cc_final: 0.7363 (m110) REVERT: e 74 LYS cc_start: 0.8816 (tttt) cc_final: 0.8551 (ttpp) REVERT: e 77 ASN cc_start: 0.9110 (t0) cc_final: 0.8662 (t0) REVERT: e 82 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8455 (mm110) outliers start: 121 outliers final: 52 residues processed: 1745 average time/residue: 0.3827 time to fit residues: 993.4536 Evaluate side-chains 1605 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1545 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 37 GLU Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain Q residue 34 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 42 CYS Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain e residue 43 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 82 GLN B 31 ASN B 34 ASN B 39 ASN C 39 ASN D 82 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 39 ASN H 13 GLN H 67 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 67 ASN K 34 ASN K 39 ASN L 31 ASN L 34 ASN L 82 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN N 31 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 ASN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 34 ASN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 ASN S 39 ASN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 13 GLN T 22 GLN T 31 ASN T 34 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 GLN V 39 ASN V 82 GLN W 22 GLN W 67 ASN X 82 GLN Y 39 ASN Y 67 ASN Z 22 GLN ** Z 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 ASN b 82 GLN b 87 GLN c 39 ASN c 82 GLN ** d 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN d 67 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23095 Z= 0.369 Angle : 0.623 8.112 31000 Z= 0.343 Chirality : 0.045 0.195 3472 Planarity : 0.004 0.053 3937 Dihedral : 3.938 15.240 2914 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 7.31 % Allowed : 17.41 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.15), residues: 2728 helix: 1.17 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 30 HIS 0.017 0.002 HIS S 56 PHE 0.019 0.002 PHE C 3 TYR 0.018 0.002 TYR a 78 ARG 0.006 0.001 ARG b 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1843 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1655 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7296 (tpp) cc_final: 0.7029 (tpp) REVERT: A 22 GLN cc_start: 0.8547 (mt0) cc_final: 0.8328 (mt0) REVERT: A 34 ASN cc_start: 0.8264 (t0) cc_final: 0.7976 (t0) REVERT: A 37 GLU cc_start: 0.8910 (mp0) cc_final: 0.8627 (mp0) REVERT: A 47 GLU cc_start: 0.7406 (tt0) cc_final: 0.6916 (tt0) REVERT: A 66 CYS cc_start: 0.8497 (m) cc_final: 0.8241 (m) REVERT: B 60 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8575 (mtmm) REVERT: B 74 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8710 (ptmm) REVERT: C 2 ASN cc_start: 0.7909 (m-40) cc_final: 0.7381 (m-40) REVERT: C 31 ASN cc_start: 0.8927 (m110) cc_final: 0.8671 (m110) REVERT: C 47 GLU cc_start: 0.7928 (tt0) cc_final: 0.7360 (tt0) REVERT: C 60 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8398 (mtpp) REVERT: C 83 ASP cc_start: 0.8624 (t70) cc_final: 0.8254 (t0) REVERT: D 13 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8732 (mm-40) REVERT: D 20 ILE cc_start: 0.9341 (mt) cc_final: 0.9092 (mp) REVERT: D 36 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: D 39 ASN cc_start: 0.8253 (m110) cc_final: 0.7724 (m110) REVERT: D 60 LYS cc_start: 0.8713 (mtmt) cc_final: 0.8312 (mtpp) REVERT: D 66 CYS cc_start: 0.8082 (m) cc_final: 0.7863 (m) REVERT: D 74 LYS cc_start: 0.9030 (tttt) cc_final: 0.8633 (ttpp) REVERT: D 78 TYR cc_start: 0.8765 (t80) cc_final: 0.8424 (t80) REVERT: E 1 MET cc_start: 0.6847 (tpp) cc_final: 0.6452 (tpt) REVERT: E 20 ILE cc_start: 0.9230 (mt) cc_final: 0.9004 (mp) REVERT: E 34 ASN cc_start: 0.8268 (t0) cc_final: 0.7148 (t0) REVERT: E 39 ASN cc_start: 0.8385 (m110) cc_final: 0.7885 (m-40) REVERT: E 52 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7923 (mtt90) REVERT: E 57 MET cc_start: 0.8160 (mtm) cc_final: 0.7904 (mtp) REVERT: E 60 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8477 (mtpp) REVERT: E 78 TYR cc_start: 0.8948 (t80) cc_final: 0.8569 (t80) REVERT: F 2 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: F 34 ASN cc_start: 0.7801 (t0) cc_final: 0.6897 (t0) REVERT: F 39 ASN cc_start: 0.8813 (m-40) cc_final: 0.8580 (m110) REVERT: G 67 ASN cc_start: 0.8843 (m-40) cc_final: 0.8632 (m110) REVERT: G 75 GLU cc_start: 0.8150 (tt0) cc_final: 0.7828 (tt0) REVERT: G 83 ASP cc_start: 0.8538 (t70) cc_final: 0.8211 (t0) REVERT: H 2 ASN cc_start: 0.7822 (m-40) cc_final: 0.7270 (m110) REVERT: H 31 ASN cc_start: 0.9152 (m-40) cc_final: 0.8950 (m-40) REVERT: H 34 ASN cc_start: 0.7948 (t0) cc_final: 0.7429 (t0) REVERT: H 36 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: H 60 LYS cc_start: 0.8528 (mtmt) cc_final: 0.7870 (mtpt) REVERT: I 54 ILE cc_start: 0.9564 (tt) cc_final: 0.9320 (mm) REVERT: I 57 MET cc_start: 0.7940 (mtp) cc_final: 0.7684 (mtp) REVERT: I 89 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7166 (tt) REVERT: J 60 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8422 (mttt) REVERT: K 13 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8324 (mm110) REVERT: K 17 MET cc_start: 0.8237 (tpp) cc_final: 0.7892 (tpp) REVERT: K 21 LYS cc_start: 0.9121 (mttt) cc_final: 0.8446 (mttp) REVERT: K 25 ASP cc_start: 0.8124 (m-30) cc_final: 0.7629 (m-30) REVERT: K 34 ASN cc_start: 0.8050 (t0) cc_final: 0.7633 (t0) REVERT: K 37 GLU cc_start: 0.8927 (mp0) cc_final: 0.8340 (mp0) REVERT: K 60 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8110 (mtpp) REVERT: K 77 ASN cc_start: 0.9123 (t0) cc_final: 0.8692 (t0) REVERT: K 83 ASP cc_start: 0.8742 (t70) cc_final: 0.8325 (t0) REVERT: L 33 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8939 (mp) REVERT: L 71 LYS cc_start: 0.9233 (ttmm) cc_final: 0.8953 (ttpp) REVERT: L 89 LEU cc_start: 0.7783 (tp) cc_final: 0.7543 (tp) REVERT: M 34 ASN cc_start: 0.8089 (t0) cc_final: 0.7716 (t0) REVERT: M 35 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7437 (tpp80) REVERT: M 39 ASN cc_start: 0.8666 (m110) cc_final: 0.8244 (m110) REVERT: M 48 GLN cc_start: 0.8721 (mp10) cc_final: 0.8363 (mp10) REVERT: M 60 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8398 (mtpp) REVERT: N 1 MET cc_start: 0.6845 (tpt) cc_final: 0.6121 (tpt) REVERT: N 34 ASN cc_start: 0.7934 (t0) cc_final: 0.6899 (t0) REVERT: N 60 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8277 (mtpt) REVERT: N 71 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9090 (ttpp) REVERT: N 89 LEU cc_start: 0.6813 (tp) cc_final: 0.6450 (tp) REVERT: O 35 ARG cc_start: 0.7649 (ttm110) cc_final: 0.7438 (ttm110) REVERT: O 39 ASN cc_start: 0.8685 (m110) cc_final: 0.8407 (m110) REVERT: O 44 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7777 (mm-30) REVERT: O 60 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8636 (mttt) REVERT: P 13 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8446 (mm-40) REVERT: P 33 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8560 (mt) REVERT: P 47 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: P 48 GLN cc_start: 0.8517 (mp10) cc_final: 0.8232 (mp10) REVERT: P 57 MET cc_start: 0.8552 (mtm) cc_final: 0.8346 (mtp) REVERT: P 60 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8727 (mtpt) REVERT: P 66 CYS cc_start: 0.8475 (m) cc_final: 0.8148 (m) REVERT: P 67 ASN cc_start: 0.8963 (m-40) cc_final: 0.8532 (m-40) REVERT: Q 60 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8824 (mtpt) REVERT: Q 71 LYS cc_start: 0.9170 (ttpp) cc_final: 0.8895 (ttpp) REVERT: R 34 ASN cc_start: 0.7829 (t0) cc_final: 0.7565 (t0) REVERT: R 36 GLU cc_start: 0.7166 (mp0) cc_final: 0.6343 (mp0) REVERT: R 44 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7590 (mm-30) REVERT: R 60 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8424 (mttt) REVERT: S 2 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7743 (m-40) REVERT: S 24 THR cc_start: 0.9310 (m) cc_final: 0.8996 (p) REVERT: S 34 ASN cc_start: 0.8146 (t0) cc_final: 0.7730 (t0) REVERT: S 37 GLU cc_start: 0.8730 (mp0) cc_final: 0.8379 (mp0) REVERT: S 60 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8467 (mtpt) REVERT: S 66 CYS cc_start: 0.8416 (m) cc_final: 0.8142 (m) REVERT: T 34 ASN cc_start: 0.8171 (t0) cc_final: 0.7686 (t0) REVERT: U 1 MET cc_start: 0.6421 (tpp) cc_final: 0.6120 (tpt) REVERT: U 39 ASN cc_start: 0.8380 (m110) cc_final: 0.7795 (m110) REVERT: U 47 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: U 49 ASP cc_start: 0.8614 (m-30) cc_final: 0.8383 (m-30) REVERT: U 60 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8321 (mtpp) REVERT: V 2 ASN cc_start: 0.8152 (m-40) cc_final: 0.7852 (m-40) REVERT: V 9 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8455 (mtp85) REVERT: V 34 ASN cc_start: 0.8102 (t0) cc_final: 0.7846 (t0) REVERT: V 35 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7674 (tpp80) REVERT: V 39 ASN cc_start: 0.8495 (m110) cc_final: 0.8031 (m-40) REVERT: V 44 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7505 (mm-30) REVERT: V 47 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: V 48 GLN cc_start: 0.8729 (mp10) cc_final: 0.8463 (mp10) REVERT: V 66 CYS cc_start: 0.8584 (m) cc_final: 0.8339 (m) REVERT: W 6 ASP cc_start: 0.8377 (m-30) cc_final: 0.8077 (m-30) REVERT: W 34 ASN cc_start: 0.8165 (t0) cc_final: 0.7905 (t0) REVERT: X 17 MET cc_start: 0.8391 (tpp) cc_final: 0.8091 (tpp) REVERT: X 21 LYS cc_start: 0.9071 (mttp) cc_final: 0.8481 (mttp) REVERT: X 25 ASP cc_start: 0.8189 (m-30) cc_final: 0.7633 (m-30) REVERT: X 34 ASN cc_start: 0.8193 (t0) cc_final: 0.7399 (t0) REVERT: X 60 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8486 (mtpt) REVERT: X 66 CYS cc_start: 0.8615 (m) cc_final: 0.8030 (m) REVERT: Y 1 MET cc_start: 0.7290 (tpp) cc_final: 0.6580 (tpt) REVERT: Y 36 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: Y 37 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: Y 43 CYS cc_start: 0.7916 (p) cc_final: 0.6852 (p) REVERT: Y 60 LYS cc_start: 0.9177 (mtmt) cc_final: 0.7959 (tptt) REVERT: Z 15 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7672 (mtp) REVERT: Z 44 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7963 (mm-30) REVERT: Z 61 LYS cc_start: 0.8926 (mttp) cc_final: 0.8707 (mttm) REVERT: a 2 ASN cc_start: 0.8214 (m-40) cc_final: 0.7985 (m110) REVERT: a 5 LYS cc_start: 0.8820 (tttm) cc_final: 0.8166 (tptt) REVERT: a 9 ARG cc_start: 0.8061 (mtp180) cc_final: 0.7596 (mmt-90) REVERT: a 57 MET cc_start: 0.8163 (ttp) cc_final: 0.7802 (ttp) REVERT: a 60 LYS cc_start: 0.9020 (mtmt) cc_final: 0.7658 (tptm) REVERT: b 1 MET cc_start: 0.6136 (tpp) cc_final: 0.5907 (tpt) REVERT: b 34 ASN cc_start: 0.7430 (t0) cc_final: 0.6848 (t0) REVERT: b 39 ASN cc_start: 0.8359 (m110) cc_final: 0.7867 (m110) REVERT: b 74 LYS cc_start: 0.9104 (ttpt) cc_final: 0.8869 (ttmm) REVERT: b 82 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8500 (mm110) REVERT: c 1 MET cc_start: 0.6809 (tpp) cc_final: 0.6511 (tpp) REVERT: c 8 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8934 (m) REVERT: c 20 ILE cc_start: 0.9140 (mt) cc_final: 0.8922 (mp) REVERT: c 34 ASN cc_start: 0.8357 (t0) cc_final: 0.7615 (t0) REVERT: c 35 ARG cc_start: 0.7853 (ttm110) cc_final: 0.7450 (ttm-80) REVERT: c 48 GLN cc_start: 0.8374 (mp10) cc_final: 0.7629 (mp10) REVERT: c 58 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8934 (tp) REVERT: c 81 PHE cc_start: 0.9174 (t80) cc_final: 0.8961 (t80) REVERT: d 13 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8826 (mm-40) REVERT: d 26 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8014 (t0) REVERT: d 60 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8270 (mtpp) REVERT: d 74 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8847 (ttpp) REVERT: d 82 GLN cc_start: 0.9128 (mm110) cc_final: 0.8835 (mm110) REVERT: d 83 ASP cc_start: 0.8556 (t70) cc_final: 0.8271 (t70) REVERT: e 13 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8595 (mm-40) REVERT: e 34 ASN cc_start: 0.8491 (t0) cc_final: 0.8138 (t0) REVERT: e 39 ASN cc_start: 0.8631 (m-40) cc_final: 0.8082 (m110) REVERT: e 74 LYS cc_start: 0.8898 (tttt) cc_final: 0.8585 (ttpp) REVERT: e 82 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8634 (mm110) outliers start: 188 outliers final: 116 residues processed: 1699 average time/residue: 0.3862 time to fit residues: 977.2766 Evaluate side-chains 1678 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1544 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 2 ASN Chi-restraints excluded: chain F residue 15 MET Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 89 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 8 SER Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 LYS Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 15 MET Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 2 ASN Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 32 VAL Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 64 GLU Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 36 GLU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 15 MET Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 58 ILE Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 54 ILE Chi-restraints excluded: chain a residue 58 ILE Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 43 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 133 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 31 ASN B 39 ASN C 22 GLN C 31 ASN D 82 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 82 GLN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN J 22 GLN J 39 ASN J 67 ASN J 82 GLN K 82 GLN L 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 ASN N 82 GLN ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 GLN Q 22 GLN R 34 ASN S 82 GLN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN V 22 GLN ** V 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 ASN W 67 ASN X 34 ASN X 67 ASN X 82 GLN Y 13 GLN Y 67 ASN Y 82 GLN Z 2 ASN Z 22 GLN Z 82 GLN a 39 ASN d 34 ASN d 39 ASN d 67 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23095 Z= 0.239 Angle : 0.576 6.277 31000 Z= 0.316 Chirality : 0.042 0.195 3472 Planarity : 0.004 0.080 3937 Dihedral : 3.879 14.275 2914 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 7.42 % Allowed : 20.25 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2728 helix: 1.20 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.82 (0.28), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 76 HIS 0.005 0.001 HIS O 56 PHE 0.018 0.001 PHE N 3 TYR 0.012 0.002 TYR c 78 ARG 0.006 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1880 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1689 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6712 (tpp) cc_final: 0.6096 (tpt) REVERT: A 14 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7472 (mtp180) REVERT: A 47 GLU cc_start: 0.7394 (tt0) cc_final: 0.6965 (tt0) REVERT: A 66 CYS cc_start: 0.8529 (m) cc_final: 0.8297 (m) REVERT: B 34 ASN cc_start: 0.8305 (p0) cc_final: 0.8066 (p0) REVERT: B 35 ARG cc_start: 0.7744 (ttp-110) cc_final: 0.7305 (tpp80) REVERT: B 37 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 39 ASN cc_start: 0.8471 (m110) cc_final: 0.7699 (m-40) REVERT: B 60 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8571 (mtmm) REVERT: C 2 ASN cc_start: 0.7992 (m-40) cc_final: 0.7656 (m-40) REVERT: C 31 ASN cc_start: 0.8885 (m-40) cc_final: 0.8636 (m110) REVERT: C 60 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8467 (mtpp) REVERT: C 78 TYR cc_start: 0.8830 (t80) cc_final: 0.8547 (t80) REVERT: C 83 ASP cc_start: 0.8564 (t70) cc_final: 0.8198 (t0) REVERT: D 13 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8630 (mm-40) REVERT: D 34 ASN cc_start: 0.8228 (t0) cc_final: 0.7885 (t0) REVERT: D 35 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7213 (tpp80) REVERT: D 39 ASN cc_start: 0.8290 (m110) cc_final: 0.7545 (m110) REVERT: D 60 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8319 (mtpp) REVERT: D 74 LYS cc_start: 0.9010 (tttt) cc_final: 0.8622 (ttpp) REVERT: D 77 ASN cc_start: 0.9252 (t0) cc_final: 0.9041 (t0) REVERT: D 78 TYR cc_start: 0.8716 (t80) cc_final: 0.8402 (t80) REVERT: E 1 MET cc_start: 0.6205 (tpp) cc_final: 0.5981 (tpp) REVERT: E 9 ARG cc_start: 0.8494 (mtp-110) cc_final: 0.8205 (mtp-110) REVERT: E 35 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7091 (tpp80) REVERT: E 39 ASN cc_start: 0.8397 (m110) cc_final: 0.7094 (m110) REVERT: E 47 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: E 57 MET cc_start: 0.8150 (mtm) cc_final: 0.7694 (mtp) REVERT: E 60 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8499 (mtpp) REVERT: E 78 TYR cc_start: 0.8663 (t80) cc_final: 0.8280 (t80) REVERT: F 34 ASN cc_start: 0.7949 (t0) cc_final: 0.7569 (t0) REVERT: F 37 GLU cc_start: 0.8701 (mp0) cc_final: 0.8434 (mp0) REVERT: G 26 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7885 (m-30) REVERT: G 34 ASN cc_start: 0.7576 (t0) cc_final: 0.7124 (t0) REVERT: G 39 ASN cc_start: 0.8630 (m110) cc_final: 0.8213 (m110) REVERT: G 52 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7591 (mtt-85) REVERT: G 83 ASP cc_start: 0.8485 (t70) cc_final: 0.8179 (t0) REVERT: H 54 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9158 (mm) REVERT: H 60 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8202 (mtpt) REVERT: I 14 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7258 (mtp180) REVERT: I 31 ASN cc_start: 0.8987 (m-40) cc_final: 0.8649 (m-40) REVERT: I 45 LYS cc_start: 0.8545 (pttt) cc_final: 0.8340 (ptmt) REVERT: J 1 MET cc_start: 0.7085 (tpp) cc_final: 0.6623 (tpt) REVERT: J 39 ASN cc_start: 0.8453 (m-40) cc_final: 0.7984 (m110) REVERT: J 65 SER cc_start: 0.9091 (m) cc_final: 0.8834 (m) REVERT: K 17 MET cc_start: 0.8288 (tpp) cc_final: 0.7999 (tpp) REVERT: K 21 LYS cc_start: 0.8911 (mttt) cc_final: 0.8326 (mttp) REVERT: K 25 ASP cc_start: 0.8131 (m-30) cc_final: 0.7462 (m-30) REVERT: K 34 ASN cc_start: 0.8173 (t0) cc_final: 0.7753 (t0) REVERT: K 37 GLU cc_start: 0.8931 (mp0) cc_final: 0.8246 (mp0) REVERT: K 60 LYS cc_start: 0.8504 (mtmt) cc_final: 0.8053 (mttt) REVERT: K 78 TYR cc_start: 0.8905 (t80) cc_final: 0.8696 (t80) REVERT: K 83 ASP cc_start: 0.8716 (t70) cc_final: 0.8341 (t0) REVERT: L 71 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8945 (ttpp) REVERT: L 74 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8783 (ptmm) REVERT: L 89 LEU cc_start: 0.7794 (tp) cc_final: 0.7553 (tp) REVERT: M 1 MET cc_start: 0.6307 (tpp) cc_final: 0.5859 (tpt) REVERT: M 5 LYS cc_start: 0.8865 (tptm) cc_final: 0.8603 (tptm) REVERT: M 36 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: M 39 ASN cc_start: 0.8360 (m110) cc_final: 0.7909 (m110) REVERT: M 60 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8437 (mtpp) REVERT: M 78 TYR cc_start: 0.8747 (t80) cc_final: 0.8482 (t80) REVERT: M 83 ASP cc_start: 0.8497 (t0) cc_final: 0.8267 (t0) REVERT: N 1 MET cc_start: 0.6239 (tpt) cc_final: 0.5706 (tpt) REVERT: N 39 ASN cc_start: 0.8644 (m-40) cc_final: 0.8313 (m-40) REVERT: N 60 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8359 (mtpp) REVERT: N 71 LYS cc_start: 0.9307 (ttmm) cc_final: 0.9093 (ptmt) REVERT: N 77 ASN cc_start: 0.9405 (t0) cc_final: 0.9108 (t0) REVERT: N 78 TYR cc_start: 0.8935 (t80) cc_final: 0.8722 (t80) REVERT: N 82 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8518 (mm110) REVERT: N 89 LEU cc_start: 0.7075 (tp) cc_final: 0.6425 (tp) REVERT: O 22 GLN cc_start: 0.8629 (mt0) cc_final: 0.8315 (mt0) REVERT: O 39 ASN cc_start: 0.8689 (m110) cc_final: 0.8337 (m110) REVERT: O 44 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7690 (mm-30) REVERT: O 60 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8663 (mttt) REVERT: P 13 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8390 (mm-40) REVERT: P 31 ASN cc_start: 0.9005 (m-40) cc_final: 0.8757 (m-40) REVERT: P 33 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8500 (mt) REVERT: P 47 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: P 48 GLN cc_start: 0.8517 (mp10) cc_final: 0.8232 (mp10) REVERT: P 57 MET cc_start: 0.8557 (mtm) cc_final: 0.8353 (mtp) REVERT: P 60 LYS cc_start: 0.9073 (mtmt) cc_final: 0.8733 (mtpt) REVERT: P 66 CYS cc_start: 0.8532 (m) cc_final: 0.8195 (m) REVERT: P 67 ASN cc_start: 0.8978 (m-40) cc_final: 0.8627 (m-40) REVERT: Q 7 ASN cc_start: 0.8808 (m-40) cc_final: 0.8131 (m110) REVERT: Q 9 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8468 (mtp85) REVERT: Q 14 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7574 (mtp180) REVERT: Q 37 GLU cc_start: 0.8690 (pm20) cc_final: 0.8346 (mp0) REVERT: Q 60 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8731 (mtpt) REVERT: Q 71 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8739 (ttpp) REVERT: R 36 GLU cc_start: 0.7153 (mp0) cc_final: 0.6361 (mp0) REVERT: R 39 ASN cc_start: 0.8644 (m-40) cc_final: 0.8402 (m110) REVERT: R 44 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7583 (mm-30) REVERT: R 60 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8559 (mttt) REVERT: R 74 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8635 (mtpp) REVERT: S 2 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8042 (m-40) REVERT: S 5 LYS cc_start: 0.8964 (tttt) cc_final: 0.8584 (tptm) REVERT: S 60 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8618 (mtpt) REVERT: S 66 CYS cc_start: 0.8570 (m) cc_final: 0.8300 (m) REVERT: S 72 SER cc_start: 0.9001 (m) cc_final: 0.8756 (t) REVERT: S 74 LYS cc_start: 0.9127 (ttpp) cc_final: 0.8901 (ttmm) REVERT: T 1 MET cc_start: 0.6830 (tpp) cc_final: 0.6282 (tpt) REVERT: T 45 LYS cc_start: 0.8290 (tttm) cc_final: 0.7810 (tttm) REVERT: T 75 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8855 (tm-30) REVERT: T 78 TYR cc_start: 0.8502 (t80) cc_final: 0.8249 (t80) REVERT: U 1 MET cc_start: 0.6067 (tpp) cc_final: 0.5780 (tpt) REVERT: U 26 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7625 (t70) REVERT: U 39 ASN cc_start: 0.8522 (m-40) cc_final: 0.7995 (m110) REVERT: U 49 ASP cc_start: 0.8538 (m-30) cc_final: 0.8309 (m-30) REVERT: U 60 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8286 (mtpp) REVERT: V 1 MET cc_start: 0.7133 (tpp) cc_final: 0.6692 (tpt) REVERT: V 2 ASN cc_start: 0.8179 (m-40) cc_final: 0.7786 (m-40) REVERT: V 5 LYS cc_start: 0.8934 (tttt) cc_final: 0.8726 (tptm) REVERT: V 35 ARG cc_start: 0.7896 (ttm170) cc_final: 0.7466 (tpp80) REVERT: V 38 VAL cc_start: 0.9094 (t) cc_final: 0.8892 (t) REVERT: V 39 ASN cc_start: 0.8433 (m110) cc_final: 0.8067 (m110) REVERT: V 44 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7425 (mm-30) REVERT: V 66 CYS cc_start: 0.8602 (m) cc_final: 0.8341 (m) REVERT: V 71 LYS cc_start: 0.9311 (ttmm) cc_final: 0.9083 (ptmt) REVERT: X 17 MET cc_start: 0.8251 (tpp) cc_final: 0.7978 (tpp) REVERT: X 21 LYS cc_start: 0.9093 (mttp) cc_final: 0.8461 (mttp) REVERT: X 25 ASP cc_start: 0.8089 (m-30) cc_final: 0.7420 (m-30) REVERT: X 34 ASN cc_start: 0.8084 (t0) cc_final: 0.7786 (t0) REVERT: X 37 GLU cc_start: 0.8865 (mp0) cc_final: 0.8622 (mp0) REVERT: X 60 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8343 (mtpt) REVERT: X 66 CYS cc_start: 0.8527 (m) cc_final: 0.7933 (m) REVERT: X 78 TYR cc_start: 0.8973 (t80) cc_final: 0.8440 (t80) REVERT: X 82 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8066 (mp10) REVERT: Y 1 MET cc_start: 0.6756 (tpp) cc_final: 0.6156 (tpt) REVERT: Y 2 ASN cc_start: 0.8323 (m-40) cc_final: 0.8015 (m110) REVERT: Y 37 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: Y 60 LYS cc_start: 0.9166 (mtmt) cc_final: 0.7895 (tptt) REVERT: Y 87 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7206 (mm-40) REVERT: Z 33 LEU cc_start: 0.8744 (mt) cc_final: 0.8524 (mt) REVERT: Z 60 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8693 (mtmt) REVERT: Z 74 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8674 (ttpp) REVERT: a 5 LYS cc_start: 0.8800 (tttm) cc_final: 0.8466 (tptt) REVERT: a 9 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7461 (mmt-90) REVERT: a 60 LYS cc_start: 0.9032 (mtmt) cc_final: 0.7670 (tptm) REVERT: b 39 ASN cc_start: 0.8360 (m110) cc_final: 0.7778 (m110) REVERT: c 1 MET cc_start: 0.6663 (tpp) cc_final: 0.6357 (tpp) REVERT: c 20 ILE cc_start: 0.9217 (mt) cc_final: 0.9013 (mp) REVERT: c 26 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7978 (t70) REVERT: c 35 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7792 (tpp80) REVERT: c 45 LYS cc_start: 0.8747 (pttt) cc_final: 0.8491 (pttt) REVERT: c 57 MET cc_start: 0.8269 (mtm) cc_final: 0.8069 (mtm) REVERT: c 58 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8914 (tp) REVERT: d 13 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8821 (mm-40) REVERT: d 26 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8142 (t70) REVERT: d 34 ASN cc_start: 0.7920 (t0) cc_final: 0.7500 (t0) REVERT: d 39 ASN cc_start: 0.8642 (m-40) cc_final: 0.8269 (m110) REVERT: d 60 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8394 (mtpp) REVERT: d 74 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8895 (ttpp) REVERT: d 82 GLN cc_start: 0.9069 (mm110) cc_final: 0.8842 (mm110) REVERT: d 83 ASP cc_start: 0.8579 (t70) cc_final: 0.8152 (t0) REVERT: e 13 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8531 (mm-40) REVERT: e 26 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8369 (t0) REVERT: e 34 ASN cc_start: 0.8593 (t0) cc_final: 0.8109 (t0) REVERT: e 39 ASN cc_start: 0.8603 (m-40) cc_final: 0.8103 (m110) outliers start: 191 outliers final: 115 residues processed: 1736 average time/residue: 0.3950 time to fit residues: 1016.1394 Evaluate side-chains 1714 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1584 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 36 GLU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 LYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 2 ASN Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 8 SER Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 15 MET Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 72 SER Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain c residue 64 GLU Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 43 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 22 GLN A 82 GLN B 31 ASN B 82 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN F 2 ASN G 31 ASN G 67 ASN G 82 GLN H 2 ASN H 82 GLN J 67 ASN K 82 GLN L 31 ASN M 31 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 GLN O 13 GLN O 22 GLN ** O 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN R 39 ASN ** T 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** U 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 GLN W 31 ASN W 67 ASN X 67 ASN Y 67 ASN Z 2 ASN Z 82 GLN a 2 ASN a 82 GLN b 22 GLN ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN e 82 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23095 Z= 0.250 Angle : 0.598 8.063 31000 Z= 0.328 Chirality : 0.042 0.186 3472 Planarity : 0.004 0.042 3937 Dihedral : 3.879 14.682 2914 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 7.15 % Allowed : 22.19 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2728 helix: 1.13 (0.10), residues: 2480 sheet: None (None), residues: 0 loop : -2.88 (0.27), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 76 HIS 0.004 0.001 HIS B 56 PHE 0.021 0.001 PHE C 3 TYR 0.011 0.002 TYR S 78 ARG 0.007 0.001 ARG R 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5456 Ramachandran restraints generated. 2728 Oldfield, 0 Emsley, 2728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1820 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1636 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6729 (tpp) cc_final: 0.6241 (tpt) REVERT: A 25 ASP cc_start: 0.8300 (m-30) cc_final: 0.7990 (m-30) REVERT: A 37 GLU cc_start: 0.8760 (mp0) cc_final: 0.8534 (mp0) REVERT: A 45 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8116 (ttpt) REVERT: A 47 GLU cc_start: 0.7497 (tt0) cc_final: 0.7083 (tt0) REVERT: A 66 CYS cc_start: 0.8503 (m) cc_final: 0.8287 (m) REVERT: B 52 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7877 (mtt-85) REVERT: B 60 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8537 (mtmm) REVERT: B 81 PHE cc_start: 0.9234 (t80) cc_final: 0.8752 (t80) REVERT: C 2 ASN cc_start: 0.8167 (m-40) cc_final: 0.7938 (m-40) REVERT: C 31 ASN cc_start: 0.8890 (m-40) cc_final: 0.8632 (m110) REVERT: C 60 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8452 (mttt) REVERT: C 78 TYR cc_start: 0.8881 (t80) cc_final: 0.8572 (t80) REVERT: C 83 ASP cc_start: 0.8519 (t70) cc_final: 0.8184 (t0) REVERT: D 1 MET cc_start: 0.6212 (tpp) cc_final: 0.5966 (tpt) REVERT: D 13 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8591 (mm-40) REVERT: D 35 ARG cc_start: 0.7702 (tpp80) cc_final: 0.7289 (tpp80) REVERT: D 39 ASN cc_start: 0.8206 (m110) cc_final: 0.7506 (m110) REVERT: D 60 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8311 (mtpp) REVERT: D 74 LYS cc_start: 0.9040 (tttt) cc_final: 0.8657 (ttpp) REVERT: D 77 ASN cc_start: 0.9268 (t0) cc_final: 0.9053 (t0) REVERT: D 78 TYR cc_start: 0.8692 (t80) cc_final: 0.8440 (t80) REVERT: E 1 MET cc_start: 0.6467 (tpp) cc_final: 0.6152 (tpt) REVERT: E 9 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8299 (mtp-110) REVERT: E 34 ASN cc_start: 0.7903 (t0) cc_final: 0.7633 (t0) REVERT: E 35 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7027 (tpp80) REVERT: E 39 ASN cc_start: 0.8489 (m110) cc_final: 0.7165 (m110) REVERT: E 47 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7197 (tt0) REVERT: E 57 MET cc_start: 0.8161 (mtm) cc_final: 0.7756 (mtp) REVERT: E 60 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8458 (mtpp) REVERT: E 74 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8692 (mtpp) REVERT: E 78 TYR cc_start: 0.8680 (t80) cc_final: 0.8262 (t80) REVERT: F 1 MET cc_start: 0.5894 (tpp) cc_final: 0.5030 (tpt) REVERT: F 2 ASN cc_start: 0.8378 (m110) cc_final: 0.7964 (m110) REVERT: F 9 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8223 (mtp-110) REVERT: G 26 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: G 35 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7706 (ttp-110) REVERT: G 39 ASN cc_start: 0.8589 (m110) cc_final: 0.8218 (m110) REVERT: G 45 LYS cc_start: 0.8310 (pttt) cc_final: 0.7922 (pttt) REVERT: G 83 ASP cc_start: 0.8484 (t70) cc_final: 0.8139 (t0) REVERT: H 13 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8992 (mm110) REVERT: H 35 ARG cc_start: 0.7616 (tpp-160) cc_final: 0.6864 (tpp-160) REVERT: H 60 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8266 (mtpt) REVERT: H 67 ASN cc_start: 0.8825 (m-40) cc_final: 0.8534 (m110) REVERT: I 1 MET cc_start: 0.5250 (tpt) cc_final: 0.5027 (tpt) REVERT: I 31 ASN cc_start: 0.8970 (m-40) cc_final: 0.8639 (m-40) REVERT: I 34 ASN cc_start: 0.7626 (t0) cc_final: 0.7165 (t0) REVERT: I 45 LYS cc_start: 0.8528 (pttt) cc_final: 0.8080 (ptmt) REVERT: J 1 MET cc_start: 0.7086 (tpp) cc_final: 0.6562 (tpt) REVERT: J 2 ASN cc_start: 0.8575 (m-40) cc_final: 0.8340 (m110) REVERT: J 39 ASN cc_start: 0.8541 (m-40) cc_final: 0.7896 (m-40) REVERT: J 65 SER cc_start: 0.9107 (m) cc_final: 0.8878 (m) REVERT: J 87 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7621 (mm-40) REVERT: K 17 MET cc_start: 0.8227 (tpp) cc_final: 0.7844 (tpt) REVERT: K 21 LYS cc_start: 0.8877 (mttt) cc_final: 0.8314 (mttp) REVERT: K 25 ASP cc_start: 0.8262 (m-30) cc_final: 0.7795 (m-30) REVERT: K 34 ASN cc_start: 0.8138 (t0) cc_final: 0.7769 (t0) REVERT: K 37 GLU cc_start: 0.8876 (mp0) cc_final: 0.7654 (mp0) REVERT: K 60 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8092 (mtpp) REVERT: K 71 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9021 (ptmt) REVERT: K 77 ASN cc_start: 0.9049 (t0) cc_final: 0.8473 (t0) REVERT: K 78 TYR cc_start: 0.8880 (t80) cc_final: 0.8673 (t80) REVERT: K 83 ASP cc_start: 0.8557 (t70) cc_final: 0.8164 (t0) REVERT: L 71 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8932 (ttpp) REVERT: L 74 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8749 (ptmm) REVERT: L 89 LEU cc_start: 0.7792 (tp) cc_final: 0.7525 (tp) REVERT: M 1 MET cc_start: 0.6370 (tpp) cc_final: 0.6153 (tpt) REVERT: M 11 LEU cc_start: 0.9015 (mt) cc_final: 0.8791 (mt) REVERT: M 35 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7500 (tpp-160) REVERT: M 39 ASN cc_start: 0.8324 (m110) cc_final: 0.7659 (m110) REVERT: M 48 GLN cc_start: 0.8703 (mp10) cc_final: 0.8247 (mp10) REVERT: M 60 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8503 (mtpp) REVERT: N 1 MET cc_start: 0.5888 (tpt) cc_final: 0.5032 (tpt) REVERT: N 39 ASN cc_start: 0.8601 (m-40) cc_final: 0.8230 (m110) REVERT: N 56 HIS cc_start: 0.8148 (m-70) cc_final: 0.7489 (m-70) REVERT: N 60 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8384 (mtpp) REVERT: N 78 TYR cc_start: 0.8939 (t80) cc_final: 0.8732 (t80) REVERT: N 82 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8514 (mm110) REVERT: N 89 LEU cc_start: 0.7434 (tp) cc_final: 0.7180 (tp) REVERT: O 39 ASN cc_start: 0.8564 (m110) cc_final: 0.8164 (m110) REVERT: O 44 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7714 (mm-30) REVERT: O 60 LYS cc_start: 0.9012 (mtmt) cc_final: 0.8730 (mttt) REVERT: P 5 LYS cc_start: 0.9204 (tptm) cc_final: 0.8748 (tptm) REVERT: P 31 ASN cc_start: 0.9027 (m-40) cc_final: 0.8778 (m-40) REVERT: P 47 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: P 48 GLN cc_start: 0.8586 (mp10) cc_final: 0.8274 (mp10) REVERT: P 60 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8724 (mtpt) REVERT: P 66 CYS cc_start: 0.8497 (m) cc_final: 0.8122 (m) REVERT: P 67 ASN cc_start: 0.8977 (m-40) cc_final: 0.8631 (m-40) REVERT: P 82 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8184 (mp10) REVERT: Q 7 ASN cc_start: 0.8794 (m-40) cc_final: 0.8125 (m110) REVERT: Q 9 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8517 (mtp85) REVERT: Q 14 ARG cc_start: 0.8047 (mtp180) cc_final: 0.7672 (mtp180) REVERT: Q 15 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7668 (ttp) REVERT: Q 60 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8772 (mtpt) REVERT: Q 75 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8654 (tm-30) REVERT: R 39 ASN cc_start: 0.8637 (m110) cc_final: 0.8371 (m110) REVERT: R 52 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7337 (mtt-85) REVERT: R 60 LYS cc_start: 0.9046 (mtmt) cc_final: 0.8628 (mttt) REVERT: R 74 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8644 (mtpp) REVERT: S 1 MET cc_start: 0.5884 (tpt) cc_final: 0.5272 (tpt) REVERT: S 2 ASN cc_start: 0.8307 (m-40) cc_final: 0.7818 (m-40) REVERT: S 34 ASN cc_start: 0.8446 (t0) cc_final: 0.7456 (t0) REVERT: S 37 GLU cc_start: 0.8578 (mp0) cc_final: 0.8373 (mp0) REVERT: S 60 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8451 (mtpp) REVERT: S 66 CYS cc_start: 0.8646 (m) cc_final: 0.8293 (m) REVERT: S 72 SER cc_start: 0.9061 (m) cc_final: 0.8774 (t) REVERT: S 74 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8908 (ttmm) REVERT: T 1 MET cc_start: 0.6572 (tpp) cc_final: 0.6004 (tpt) REVERT: T 2 ASN cc_start: 0.8280 (m-40) cc_final: 0.8072 (m-40) REVERT: T 37 GLU cc_start: 0.8764 (pm20) cc_final: 0.8479 (pm20) REVERT: T 39 ASN cc_start: 0.8458 (m110) cc_final: 0.7589 (m110) REVERT: T 45 LYS cc_start: 0.8226 (tttm) cc_final: 0.7725 (tttm) REVERT: U 25 ASP cc_start: 0.8034 (m-30) cc_final: 0.7569 (m-30) REVERT: U 26 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7624 (t70) REVERT: U 35 ARG cc_start: 0.7364 (tpt90) cc_final: 0.6942 (tpt90) REVERT: U 39 ASN cc_start: 0.8678 (m-40) cc_final: 0.8241 (m110) REVERT: U 44 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7704 (mm-30) REVERT: U 47 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: U 49 ASP cc_start: 0.8570 (m-30) cc_final: 0.8031 (m-30) REVERT: U 60 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8368 (mtpp) REVERT: U 74 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8718 (ptmm) REVERT: V 1 MET cc_start: 0.7228 (tpp) cc_final: 0.6959 (tpt) REVERT: V 2 ASN cc_start: 0.8276 (m-40) cc_final: 0.7977 (m-40) REVERT: V 35 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7336 (tpp80) REVERT: V 39 ASN cc_start: 0.8425 (m110) cc_final: 0.8032 (m110) REVERT: V 44 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7410 (mm-30) REVERT: V 66 CYS cc_start: 0.8499 (m) cc_final: 0.8228 (m) REVERT: V 71 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9086 (ptmt) REVERT: W 34 ASN cc_start: 0.8114 (t0) cc_final: 0.7786 (t0) REVERT: X 14 ARG cc_start: 0.7802 (mtt180) cc_final: 0.6379 (tpt170) REVERT: X 17 MET cc_start: 0.8239 (tpp) cc_final: 0.7989 (tpp) REVERT: X 21 LYS cc_start: 0.9121 (mttp) cc_final: 0.8479 (mttp) REVERT: X 25 ASP cc_start: 0.8165 (m-30) cc_final: 0.7588 (m-30) REVERT: X 35 ARG cc_start: 0.7831 (tpp-160) cc_final: 0.7231 (tpp-160) REVERT: X 60 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8363 (mtpt) REVERT: X 66 CYS cc_start: 0.8587 (m) cc_final: 0.7944 (m) REVERT: Y 1 MET cc_start: 0.6895 (tpp) cc_final: 0.6381 (tpt) REVERT: Y 7 ASN cc_start: 0.8878 (m-40) cc_final: 0.8345 (m-40) REVERT: Y 37 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: Y 60 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8061 (tmtt) REVERT: Y 87 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7394 (mm-40) REVERT: Z 60 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8754 (mtpt) REVERT: Z 74 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8718 (ttpp) REVERT: a 5 LYS cc_start: 0.8846 (tttm) cc_final: 0.8527 (tptt) REVERT: a 9 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7463 (mmt-90) REVERT: a 57 MET cc_start: 0.8133 (ttp) cc_final: 0.7766 (ttp) REVERT: a 60 LYS cc_start: 0.9035 (mtmt) cc_final: 0.7689 (tptm) REVERT: b 39 ASN cc_start: 0.8376 (m110) cc_final: 0.7759 (m110) REVERT: b 74 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8785 (ptmm) REVERT: c 1 MET cc_start: 0.6746 (tpp) cc_final: 0.5964 (tpt) REVERT: c 20 ILE cc_start: 0.9223 (mt) cc_final: 0.9004 (mp) REVERT: c 26 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7963 (t70) REVERT: c 35 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7521 (tpp80) REVERT: c 48 GLN cc_start: 0.8277 (mp10) cc_final: 0.7762 (mp10) REVERT: c 58 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8955 (tp) REVERT: d 13 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8830 (mm-40) REVERT: d 26 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7986 (t0) REVERT: d 39 ASN cc_start: 0.8671 (m-40) cc_final: 0.8292 (m110) REVERT: d 56 HIS cc_start: 0.7902 (m-70) cc_final: 0.7380 (m-70) REVERT: d 60 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8469 (mtpp) REVERT: d 74 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8896 (ttpp) REVERT: d 82 GLN cc_start: 0.9076 (mm110) cc_final: 0.8830 (mm110) REVERT: d 83 ASP cc_start: 0.8597 (t70) cc_final: 0.8166 (t0) REVERT: d 87 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8105 (mm-40) REVERT: e 13 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8476 (mm-40) REVERT: e 34 ASN cc_start: 0.8597 (t0) cc_final: 0.8295 (t0) REVERT: e 39 ASN cc_start: 0.8489 (m-40) cc_final: 0.7915 (m110) outliers start: 184 outliers final: 127 residues processed: 1683 average time/residue: 0.3875 time to fit residues: 963.3101 Evaluate side-chains 1722 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1580 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain H residue 15 MET Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 47 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 72 SER Chi-restraints excluded: chain K residue 8 SER Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 55 ILE Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 LYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain O residue 36 GLU Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 71 LYS Chi-restraints excluded: chain P residue 36 GLU Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain Q residue 8 SER Chi-restraints excluded: chain Q residue 15 MET Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 47 GLU Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 47 GLU Chi-restraints excluded: chain U residue 8 SER Chi-restraints excluded: chain U residue 26 ASP Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 74 LYS Chi-restraints excluded: chain V residue 8 SER Chi-restraints excluded: chain V residue 15 MET Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 32 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 54 ILE Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 72 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 32 VAL Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 18 THR Chi-restraints excluded: chain X residue 26 ASP Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain Y residue 63 SER Chi-restraints excluded: chain Y residue 64 GLU Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Z residue 47 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain a residue 15 MET Chi-restraints excluded: chain a residue 33 LEU Chi-restraints excluded: chain a residue 37 GLU Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain b residue 18 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain b residue 47 GLU Chi-restraints excluded: chain b residue 58 ILE Chi-restraints excluded: chain b residue 63 SER Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 18 THR Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 47 GLU Chi-restraints excluded: chain c residue 58 ILE Chi-restraints excluded: chain d residue 8 SER Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 36 GLU Chi-restraints excluded: chain d residue 58 ILE Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 74 LYS Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 43 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: