Starting phenix.real_space_refine on Sun Aug 9 00:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.map" model { file = "/net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vf4_65024/08_2026/9vf4_65024.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 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 110 5.16 5 C 20790 2.51 5 N 5115 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31570 Number of models: 1 Model: "" Number of chains: 1 Chain: "c" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 574 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Restraints were copied for chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, a, b, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s Time building chain proxies: 2.93, per 1000 atoms: 0.09 Number of scatterers: 31570 At special positions: 0 Unit cell: (90, 91.2, 219.6, 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 110 16.00 O 5555 8.00 N 5115 7.00 C 20790 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 Links applied TRANS " SER 0 1 " - " GLY 0 78 " " SER 1 1 " - " GLY 1 78 " " SER 2 1 " - " GLY 2 78 " " SER 3 1 " - " GLY 3 78 " " SER 4 1 " - " GLY 4 78 " " SER 5 1 " - " GLY 5 78 " " SER 6 1 " - " GLY 6 78 " " SER 7 1 " - " GLY 7 78 " " SER 8 1 " - " GLY 8 78 " " SER 9 1 " - " GLY 9 78 " " SER A 1 " - " GLY A 78 " " SER B 1 " - " GLY B 78 " " SER C 1 " - " GLY C 78 " " SER D 1 " - " GLY D 78 " " SER E 1 " - " GLY E 78 " " SER F 1 " - " GLY F 78 " " SER G 1 " - " GLY G 78 " " SER H 1 " - " GLY H 78 " " SER I 1 " - " GLY I 78 " " SER J 1 " - " GLY J 78 " " SER K 1 " - " GLY K 78 " " SER L 1 " - " GLY L 78 " " SER M 1 " - " GLY M 78 " " SER N 1 " - " GLY N 78 " " SER O 1 " - " GLY O 78 " " SER P 1 " - " GLY P 78 " " SER Q 1 " - " GLY Q 78 " " SER R 1 " - " GLY R 78 " " SER S 1 " - " GLY S 78 " " SER T 1 " - " GLY T 78 " " SER U 1 " - " GLY U 78 " " SER V 1 " - " GLY V 78 " " SER W 1 " - " GLY W 78 " " SER X 1 " - " GLY X 78 " " SER Y 1 " - " GLY Y 78 " " SER Z 1 " - " GLY Z 78 " " SER a 1 " - " GLY a 78 " " SER b 1 " - " GLY b 78 " " SER c 1 " - " GLY c 78 " " SER d 1 " - " GLY d 78 " " SER e 1 " - " GLY e 78 " " SER f 1 " - " GLY f 78 " " SER g 1 " - " GLY g 78 " " SER h 1 " - " GLY h 78 " " SER i 1 " - " GLY i 78 " " SER j 1 " - " GLY j 78 " " SER k 1 " - " GLY k 78 " " SER l 1 " - " GLY l 78 " " SER m 1 " - " GLY m 78 " " SER n 1 " - " GLY n 78 " " SER o 1 " - " GLY o 78 " " SER p 1 " - " GLY p 78 " " SER q 1 " - " GLY q 78 " " SER r 1 " - " GLY r 78 " " SER s 1 " - " GLY s 78 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.3 seconds 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7260 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'c' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP c 13 " --> pdb=" O PRO c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE c 43 " --> pdb=" O GLY c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA c 62 " --> pdb=" O VAL c 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU c 63 " --> pdb=" O LEU c 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU c 64 " --> pdb=" O VAL c 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 73 Processing helix chain 'A' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE A 43 " --> pdb=" O GLY A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'B' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP B 13 " --> pdb=" O PRO B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE B 43 " --> pdb=" O GLY B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'C' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE C 43 " --> pdb=" O GLY C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 64 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'D' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP D 13 " --> pdb=" O PRO D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE D 43 " --> pdb=" O GLY D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'E' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE E 43 " --> pdb=" O GLY E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU E 64 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 Processing helix chain 'F' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP F 13 " --> pdb=" O PRO F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'G' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP G 13 " --> pdb=" O PRO G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE G 43 " --> pdb=" O GLY G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA G 62 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU G 64 " --> pdb=" O VAL G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 73 Processing helix chain 'H' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP H 13 " --> pdb=" O PRO H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE H 43 " --> pdb=" O GLY H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA H 62 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 73 Processing helix chain 'I' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP I 13 " --> pdb=" O PRO I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE I 43 " --> pdb=" O GLY I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA I 62 " --> pdb=" O VAL I 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 64 " --> pdb=" O VAL I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 73 Processing helix chain 'J' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP J 13 " --> pdb=" O PRO J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA J 62 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 64 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 73 Processing helix chain 'K' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP K 13 " --> pdb=" O PRO K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA K 62 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU K 63 " --> pdb=" O LEU K 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 73 Processing helix chain 'L' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP L 13 " --> pdb=" O PRO L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE L 43 " --> pdb=" O GLY L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA L 62 " --> pdb=" O VAL L 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU L 63 " --> pdb=" O LEU L 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 73 Processing helix chain 'M' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP M 13 " --> pdb=" O PRO M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE M 43 " --> pdb=" O GLY M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA M 62 " --> pdb=" O VAL M 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 73 Processing helix chain 'N' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP N 13 " --> pdb=" O PRO N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA N 62 " --> pdb=" O VAL N 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 73 Processing helix chain 'O' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP O 13 " --> pdb=" O PRO O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE O 43 " --> pdb=" O GLY O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA O 62 " --> pdb=" O VAL O 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU O 63 " --> pdb=" O LEU O 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU O 64 " --> pdb=" O VAL O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 73 Processing helix chain 'P' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP P 13 " --> pdb=" O PRO P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE P 43 " --> pdb=" O GLY P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA P 62 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 73 Processing helix chain 'Q' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP Q 13 " --> pdb=" O PRO Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE Q 43 " --> pdb=" O GLY Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA Q 62 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Q 64 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 73 Processing helix chain 'R' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP R 13 " --> pdb=" O PRO R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 73 Processing helix chain 'S' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP S 13 " --> pdb=" O PRO S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE S 43 " --> pdb=" O GLY S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA S 62 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU S 63 " --> pdb=" O LEU S 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU S 64 " --> pdb=" O VAL S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 73 Processing helix chain 'T' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP T 13 " --> pdb=" O PRO T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE T 43 " --> pdb=" O GLY T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA T 62 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU T 63 " --> pdb=" O LEU T 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU T 64 " --> pdb=" O VAL T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'U' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP U 13 " --> pdb=" O PRO U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE U 43 " --> pdb=" O GLY U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA U 62 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU U 63 " --> pdb=" O LEU U 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU U 64 " --> pdb=" O VAL U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 73 Processing helix chain 'V' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP V 13 " --> pdb=" O PRO V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE V 43 " --> pdb=" O GLY V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA V 62 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU V 63 " --> pdb=" O LEU V 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU V 64 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 73 Processing helix chain 'W' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP W 13 " --> pdb=" O PRO W 9 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE W 43 " --> pdb=" O GLY W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA W 62 " --> pdb=" O VAL W 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU W 63 " --> pdb=" O LEU W 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU W 64 " --> pdb=" O VAL W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 73 Processing helix chain 'X' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP X 13 " --> pdb=" O PRO X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE X 43 " --> pdb=" O GLY X 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA X 62 " --> pdb=" O VAL X 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU X 63 " --> pdb=" O LEU X 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU X 64 " --> pdb=" O VAL X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 73 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP Y 13 " --> pdb=" O PRO Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE Y 43 " --> pdb=" O GLY Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA Y 62 " --> pdb=" O VAL Y 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU Y 63 " --> pdb=" O LEU Y 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Y 64 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 73 Processing helix chain 'Z' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP Z 13 " --> pdb=" O PRO Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE Z 43 " --> pdb=" O GLY Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA Z 62 " --> pdb=" O VAL Z 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU Z 63 " --> pdb=" O LEU Z 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU Z 64 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 66 through 73 Processing helix chain '0' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 0 13 " --> pdb=" O PRO 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 0 43 " --> pdb=" O GLY 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 0 62 " --> pdb=" O VAL 0 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 0 63 " --> pdb=" O LEU 0 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 0 64 " --> pdb=" O VAL 0 60 " (cutoff:3.500A) Processing helix chain '0' and resid 66 through 73 Processing helix chain '1' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 1 13 " --> pdb=" O PRO 1 9 " (cutoff:3.500A) Processing helix chain '1' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 1 43 " --> pdb=" O GLY 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 1 62 " --> pdb=" O VAL 1 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU 1 63 " --> pdb=" O LEU 1 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 1 64 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) Processing helix chain '1' and resid 66 through 73 Processing helix chain '2' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 2 43 " --> pdb=" O GLY 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 2 62 " --> pdb=" O VAL 2 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 2 63 " --> pdb=" O LEU 2 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 2 64 " --> pdb=" O VAL 2 60 " (cutoff:3.500A) Processing helix chain '2' and resid 66 through 73 Processing helix chain '3' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP 3 13 " --> pdb=" O PRO 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 3 43 " --> pdb=" O GLY 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 3 62 " --> pdb=" O VAL 3 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 73 Processing helix chain '4' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 4 13 " --> pdb=" O PRO 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 4 43 " --> pdb=" O GLY 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 4 62 " --> pdb=" O VAL 4 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 4 63 " --> pdb=" O LEU 4 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 4 64 " --> pdb=" O VAL 4 60 " (cutoff:3.500A) Processing helix chain '4' and resid 66 through 73 Processing helix chain '5' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 5 13 " --> pdb=" O PRO 5 9 " (cutoff:3.500A) Processing helix chain '5' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 5 43 " --> pdb=" O GLY 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 5 62 " --> pdb=" O VAL 5 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 5 63 " --> pdb=" O LEU 5 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 5 64 " --> pdb=" O VAL 5 60 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 73 Processing helix chain '6' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 6 13 " --> pdb=" O PRO 6 9 " (cutoff:3.500A) Processing helix chain '6' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 6 43 " --> pdb=" O GLY 6 39 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 6 62 " --> pdb=" O VAL 6 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 6 63 " --> pdb=" O LEU 6 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 6 64 " --> pdb=" O VAL 6 60 " (cutoff:3.500A) Processing helix chain '6' and resid 66 through 73 Processing helix chain '7' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 7 13 " --> pdb=" O PRO 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 7 43 " --> pdb=" O GLY 7 39 " (cutoff:3.500A) Processing helix chain '7' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 7 62 " --> pdb=" O VAL 7 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 7 63 " --> pdb=" O LEU 7 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU 7 64 " --> pdb=" O VAL 7 60 " (cutoff:3.500A) Processing helix chain '7' and resid 66 through 73 Processing helix chain '8' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 8 13 " --> pdb=" O PRO 8 9 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE 8 43 " --> pdb=" O GLY 8 39 " (cutoff:3.500A) Processing helix chain '8' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 8 62 " --> pdb=" O VAL 8 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 8 63 " --> pdb=" O LEU 8 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 8 64 " --> pdb=" O VAL 8 60 " (cutoff:3.500A) Processing helix chain '8' and resid 66 through 73 Processing helix chain '9' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP 9 13 " --> pdb=" O PRO 9 9 " (cutoff:3.500A) Processing helix chain '9' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE 9 43 " --> pdb=" O GLY 9 39 " (cutoff:3.500A) Processing helix chain '9' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA 9 62 " --> pdb=" O VAL 9 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU 9 63 " --> pdb=" O LEU 9 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 9 64 " --> pdb=" O VAL 9 60 " (cutoff:3.500A) Processing helix chain '9' and resid 66 through 73 Processing helix chain 'a' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP a 13 " --> pdb=" O PRO a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE a 43 " --> pdb=" O GLY a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA a 62 " --> pdb=" O VAL a 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU a 64 " --> pdb=" O VAL a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 73 Processing helix chain 'b' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP b 13 " --> pdb=" O PRO b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA b 62 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU b 63 " --> pdb=" O LEU b 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'd' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP d 13 " --> pdb=" O PRO d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE d 43 " --> pdb=" O GLY d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA d 62 " --> pdb=" O VAL d 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU d 63 " --> pdb=" O LEU d 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU d 64 " --> pdb=" O VAL d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 73 Processing helix chain 'e' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP e 13 " --> pdb=" O PRO e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE e 43 " --> pdb=" O GLY e 39 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA e 62 " --> pdb=" O VAL e 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU e 63 " --> pdb=" O LEU e 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU e 64 " --> pdb=" O VAL e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 73 Processing helix chain 'f' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP f 13 " --> pdb=" O PRO f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE f 43 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA f 62 " --> pdb=" O VAL f 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU f 64 " --> pdb=" O VAL f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 73 Processing helix chain 'g' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP g 13 " --> pdb=" O PRO g 9 " (cutoff:3.500A) Processing helix chain 'g' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE g 43 " --> pdb=" O GLY g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA g 62 " --> pdb=" O VAL g 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU g 63 " --> pdb=" O LEU g 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU g 64 " --> pdb=" O VAL g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 73 Processing helix chain 'h' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP h 13 " --> pdb=" O PRO h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE h 43 " --> pdb=" O GLY h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA h 62 " --> pdb=" O VAL h 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU h 63 " --> pdb=" O LEU h 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU h 64 " --> pdb=" O VAL h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 73 Processing helix chain 'i' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP i 13 " --> pdb=" O PRO i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA i 62 " --> pdb=" O VAL i 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU i 63 " --> pdb=" O LEU i 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU i 64 " --> pdb=" O VAL i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 73 Processing helix chain 'j' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP j 13 " --> pdb=" O PRO j 9 " (cutoff:3.500A) Processing helix chain 'j' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE j 43 " --> pdb=" O GLY j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA j 62 " --> pdb=" O VAL j 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU j 63 " --> pdb=" O LEU j 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 73 Processing helix chain 'k' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP k 13 " --> pdb=" O PRO k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE k 43 " --> pdb=" O GLY k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA k 62 " --> pdb=" O VAL k 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU k 63 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU k 64 " --> pdb=" O VAL k 60 " (cutoff:3.500A) Processing helix chain 'k' and resid 66 through 73 Processing helix chain 'l' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP l 13 " --> pdb=" O PRO l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE l 43 " --> pdb=" O GLY l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA l 62 " --> pdb=" O VAL l 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 73 Processing helix chain 'm' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP m 13 " --> pdb=" O PRO m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE m 43 " --> pdb=" O GLY m 39 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA m 62 " --> pdb=" O VAL m 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU m 63 " --> pdb=" O LEU m 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 73 Processing helix chain 'n' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP n 13 " --> pdb=" O PRO n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE n 43 " --> pdb=" O GLY n 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA n 62 " --> pdb=" O VAL n 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU n 63 " --> pdb=" O LEU n 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 73 Processing helix chain 'o' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP o 13 " --> pdb=" O PRO o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE o 43 " --> pdb=" O GLY o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA o 62 " --> pdb=" O VAL o 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU o 63 " --> pdb=" O LEU o 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU o 64 " --> pdb=" O VAL o 60 " (cutoff:3.500A) Processing helix chain 'o' and resid 66 through 73 Processing helix chain 'p' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP p 13 " --> pdb=" O PRO p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE p 43 " --> pdb=" O GLY p 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA p 62 " --> pdb=" O VAL p 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU p 63 " --> pdb=" O LEU p 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU p 64 " --> pdb=" O VAL p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 73 Processing helix chain 'q' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP q 13 " --> pdb=" O PRO q 9 " (cutoff:3.500A) Processing helix chain 'q' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE q 43 " --> pdb=" O GLY q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA q 62 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU q 63 " --> pdb=" O LEU q 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU q 64 " --> pdb=" O VAL q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 73 Processing helix chain 'r' and resid 9 through 23 removed outlier: 4.001A pdb=" N TRP r 13 " --> pdb=" O PRO r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 23 through 43 removed outlier: 4.247A pdb=" N PHE r 43 " --> pdb=" O GLY r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA r 62 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU r 63 " --> pdb=" O LEU r 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 73 Processing helix chain 's' and resid 9 through 23 removed outlier: 4.000A pdb=" N TRP s 13 " --> pdb=" O PRO s 9 " (cutoff:3.500A) Processing helix chain 's' and resid 23 through 43 removed outlier: 4.248A pdb=" N PHE s 43 " --> pdb=" O GLY s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 46 through 65 removed outlier: 4.006A pdb=" N ALA s 62 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU s 63 " --> pdb=" O LEU s 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU s 64 " --> pdb=" O VAL s 60 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 73 2365 hydrogen bonds defined for protein. 7095 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: 6.25 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9900 1.34 - 1.46: 5226 1.46 - 1.57: 16829 1.57 - 1.69: 0 1.69 - 1.80: 220 Bond restraints: 32175 Sorted by residual: bond pdb=" CG1 ILE q 42 " pdb=" CD1 ILE q 42 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.16e-01 bond pdb=" CG1 ILE I 42 " pdb=" CD1 ILE I 42 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.10e-01 bond pdb=" CG1 ILE W 42 " pdb=" CD1 ILE W 42 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.08e-01 bond pdb=" CG1 ILE 4 42 " pdb=" CD1 ILE 4 42 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.07e-01 bond pdb=" CG1 ILE X 42 " pdb=" CD1 ILE X 42 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.07e-01 ... (remaining 32170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 38523 0.68 - 1.37: 3976 1.37 - 2.05: 896 2.05 - 2.73: 55 2.73 - 3.42: 220 Bond angle restraints: 43670 Sorted by residual: angle pdb=" N GLY L 66 " pdb=" CA GLY L 66 " pdb=" C GLY L 66 " ideal model delta sigma weight residual 113.18 116.60 -3.42 2.37e+00 1.78e-01 2.08e+00 angle pdb=" N GLY E 66 " pdb=" CA GLY E 66 " pdb=" C GLY E 66 " ideal model delta sigma weight residual 113.18 116.58 -3.40 2.37e+00 1.78e-01 2.06e+00 angle pdb=" N GLY K 66 " pdb=" CA GLY K 66 " pdb=" C GLY K 66 " ideal model delta sigma weight residual 113.18 116.57 -3.39 2.37e+00 1.78e-01 2.05e+00 angle pdb=" N GLY H 66 " pdb=" CA GLY H 66 " pdb=" C GLY H 66 " ideal model delta sigma weight residual 113.18 116.57 -3.39 2.37e+00 1.78e-01 2.05e+00 angle pdb=" N GLY 2 66 " pdb=" CA GLY 2 66 " pdb=" C GLY 2 66 " ideal model delta sigma weight residual 113.18 116.57 -3.39 2.37e+00 1.78e-01 2.05e+00 ... (remaining 43665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 15574 17.30 - 34.60: 2191 34.60 - 51.91: 165 51.91 - 69.21: 165 69.21 - 86.51: 55 Dihedral angle restraints: 18150 sinusoidal: 6545 harmonic: 11605 Sorted by residual: dihedral pdb=" CA SER P 1 " pdb=" N SER P 1 " pdb=" C GLY P 78 " pdb=" CA GLY P 78 " ideal model delta harmonic sigma weight residual -180.00 -127.25 -52.75 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA SER U 1 " pdb=" N SER U 1 " pdb=" C GLY U 78 " pdb=" CA GLY U 78 " ideal model delta harmonic sigma weight residual -180.00 -127.26 -52.74 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA SER N 1 " pdb=" N SER N 1 " pdb=" C GLY N 78 " pdb=" CA GLY N 78 " ideal model delta harmonic sigma weight residual -180.00 -127.26 -52.74 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 18147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2365 0.025 - 0.050: 1966 0.050 - 0.075: 561 0.075 - 0.100: 251 0.100 - 0.125: 137 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA PRO T 24 " pdb=" N PRO T 24 " pdb=" C PRO T 24 " pdb=" CB PRO T 24 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA PRO i 24 " pdb=" N PRO i 24 " pdb=" C PRO i 24 " pdb=" CB PRO i 24 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA PRO 9 24 " pdb=" N PRO 9 24 " pdb=" C PRO 9 24 " pdb=" CB PRO 9 24 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 5277 not shown) Planarity restraints: 5500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N SER N 1 " -0.019 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" CA GLY N 78 " -0.018 2.00e-02 2.50e+03 pdb=" C GLY N 78 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY N 78 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SER f 1 " -0.019 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" CA GLY f 78 " -0.018 2.00e-02 2.50e+03 pdb=" C GLY f 78 " 0.055 2.00e-02 2.50e+03 pdb=" O GLY f 78 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N SER p 1 " 0.019 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" CA GLY p 78 " 0.018 2.00e-02 2.50e+03 pdb=" C GLY p 78 " -0.055 2.00e-02 2.50e+03 pdb=" O GLY p 78 " 0.018 2.00e-02 2.50e+03 ... (remaining 5497 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1439 2.72 - 3.26: 34832 3.26 - 3.81: 57532 3.81 - 4.35: 67680 4.35 - 4.90: 120521 Nonbonded interactions: 282004 Sorted by model distance: nonbonded pdb=" O GLU A 2 " pdb=" NH1 ARG A 77 " model vdw 2.170 3.120 nonbonded pdb=" O GLU n 2 " pdb=" NH1 ARG n 77 " model vdw 2.170 3.120 nonbonded pdb=" O GLU W 2 " pdb=" NH1 ARG W 77 " model vdw 2.171 3.120 nonbonded pdb=" O GLU B 2 " pdb=" NH1 ARG B 77 " model vdw 2.171 3.120 nonbonded pdb=" O GLU 3 2 " pdb=" NH1 ARG 3 77 " model vdw 2.171 3.120 ... (remaining 281999 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: 0.14 Found NCS groups: ncs_group { reference = chain 'c' selection = 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'a' selection = chain 'b' 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' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 25.040 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.120 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.006 0.033 32230 Z= 0.260 Angle : 0.905 14.207 43835 Z= 0.513 Chirality : 0.041 0.125 5280 Planarity : 0.004 0.020 5445 Dihedral : 15.960 86.509 10725 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.67 % Allowed : 20.00 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 4180 helix: 1.45 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.01 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG 0 77 TYR 0.012 0.004 TYR s 10 PHE 0.014 0.002 PHE I 51 TRP 0.009 0.002 TRP D 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.26 (32175) covalent geometry : angle 0.50314 / 0.29 (43670) hydrogen bonds : bond 0.07680 / 5.21 ( 2365) hydrogen bonds : angle 4.57213 / 3.04 ( 7095) link_TRANS : bond 0.00058 / 0.04 ( 55) link_TRANS : angle 12.27725 / 8.41 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 997 time to evaluate : 1.092 Fit side-chains REVERT: c 68 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8389 (tp40) REVERT: A 1 SER cc_start: 0.7612 (p) cc_final: 0.7410 (p) REVERT: B 12 SER cc_start: 0.8098 (t) cc_final: 0.7880 (t) REVERT: G 2 GLU cc_start: 0.6939 (tt0) cc_final: 0.6598 (mp0) REVERT: H 2 GLU cc_start: 0.8335 (tt0) cc_final: 0.7261 (mp0) REVERT: I 61 MET cc_start: 0.8623 (mmp) cc_final: 0.8383 (mmt) REVERT: J 7 SER cc_start: 0.9023 (m) cc_final: 0.8769 (t) REVERT: J 61 MET cc_start: 0.8528 (mmp) cc_final: 0.8269 (mmm) REVERT: L 4 THR cc_start: 0.7232 (p) cc_final: 0.6981 (p) REVERT: L 68 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8479 (tp40) REVERT: N 11 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7476 (mt-10) REVERT: P 2 GLU cc_start: 0.6966 (tt0) cc_final: 0.6530 (mp0) REVERT: Q 2 GLU cc_start: 0.7981 (tt0) cc_final: 0.7084 (mp0) REVERT: R 20 SER cc_start: 0.8932 (t) cc_final: 0.8451 (p) REVERT: R 61 MET cc_start: 0.8550 (mmp) cc_final: 0.8188 (mmm) REVERT: S 11 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7807 (mt-10) REVERT: S 61 MET cc_start: 0.8738 (mmp) cc_final: 0.8387 (mmp) REVERT: U 2 GLU cc_start: 0.7081 (tt0) cc_final: 0.6633 (mp0) REVERT: U 69 ASN cc_start: 0.8815 (t0) cc_final: 0.8484 (t0) REVERT: V 2 GLU cc_start: 0.8197 (tt0) cc_final: 0.7221 (mp0) REVERT: X 1 SER cc_start: 0.7176 (p) cc_final: 0.6820 (p) REVERT: X 77 ARG cc_start: 0.7063 (tpp80) cc_final: 0.6859 (tpt-90) REVERT: Z 61 MET cc_start: 0.8523 (mmp) cc_final: 0.8198 (mmm) REVERT: Z 71 MET cc_start: 0.8581 (mmm) cc_final: 0.8377 (mmm) REVERT: 0 11 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7647 (mt-10) REVERT: 1 1 SER cc_start: 0.6992 (p) cc_final: 0.6777 (p) REVERT: 3 2 GLU cc_start: 0.7920 (tt0) cc_final: 0.7409 (mp0) REVERT: 3 32 ILE cc_start: 0.9054 (mt) cc_final: 0.8842 (mt) REVERT: 7 1 SER cc_start: 0.7268 (p) cc_final: 0.7049 (p) REVERT: 7 2 GLU cc_start: 0.6757 (tt0) cc_final: 0.6542 (mp0) REVERT: 7 69 ASN cc_start: 0.8386 (t0) cc_final: 0.8147 (t0) REVERT: d 2 GLU cc_start: 0.6882 (tt0) cc_final: 0.6298 (mp0) REVERT: d 69 ASN cc_start: 0.8570 (t0) cc_final: 0.8085 (t0) REVERT: f 61 MET cc_start: 0.8804 (mmp) cc_final: 0.8307 (mmm) REVERT: g 61 MET cc_start: 0.8304 (mmp) cc_final: 0.8015 (mmm) REVERT: i 2 GLU cc_start: 0.7249 (tt0) cc_final: 0.6869 (mp0) REVERT: j 71 MET cc_start: 0.8253 (mmm) cc_final: 0.7990 (mmm) REVERT: k 1 SER cc_start: 0.6485 (p) cc_final: 0.6200 (p) REVERT: k 7 SER cc_start: 0.8810 (m) cc_final: 0.8547 (t) REVERT: n 2 GLU cc_start: 0.7757 (tt0) cc_final: 0.7034 (mp0) REVERT: o 17 LEU cc_start: 0.8528 (tp) cc_final: 0.8318 (tp) REVERT: p 1 SER cc_start: 0.7027 (p) cc_final: 0.6821 (p) REVERT: p 18 ARG cc_start: 0.7433 (mtm110) cc_final: 0.4797 (mmt180) REVERT: p 71 MET cc_start: 0.7599 (mmm) cc_final: 0.7378 (mmm) REVERT: q 18 ARG cc_start: 0.6450 (mtm110) cc_final: 0.4548 (mmt-90) REVERT: s 18 ARG cc_start: 0.7359 (mtm110) cc_final: 0.5689 (tpt170) outliers start: 55 outliers final: 29 residues processed: 1029 average time/residue: 0.4128 time to fit residues: 547.5389 Evaluate side-chains 701 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 672 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain T residue 30 SER Chi-restraints excluded: chain U residue 31 ILE Chi-restraints excluded: chain Y residue 30 SER Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain 0 residue 30 SER Chi-restraints excluded: chain 1 residue 30 SER Chi-restraints excluded: chain 1 residue 71 MET Chi-restraints excluded: chain 2 residue 30 SER Chi-restraints excluded: chain 6 residue 30 SER Chi-restraints excluded: chain b residue 30 SER Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain h residue 10 TYR Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain m residue 10 TYR Chi-restraints excluded: chain q residue 30 SER Chi-restraints excluded: chain s residue 30 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... c 19 ASN c 69 ASN B 19 ASN G 69 ASN L 69 ASN O 69 ASN P 16 ASN P 69 ASN Q 69 ASN S 69 ASN T 69 ASN U 69 ASN V 69 ASN ** W 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 69 ASN Y 69 ASN Z 69 ASN 1 69 ASN 2 16 ASN 2 69 ASN 3 69 ASN 6 69 ASN 7 69 ASN 8 69 ASN ** 9 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 ASN b 69 ASN d 69 ASN e 69 ASN f 16 ASN g 69 ASN i 69 ASN k 69 ASN l 69 ASN n 69 ASN p 69 ASN q 69 ASN r 69 ASN s 69 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088431 restraints weight = 51941.002| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.04 r_work: 0.3088 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32230 Z= 0.131 Angle : 0.598 13.230 43835 Z= 0.295 Chirality : 0.038 0.137 5280 Planarity : 0.003 0.068 5445 Dihedral : 3.643 39.510 4496 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 4.15 % Allowed : 23.09 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.13), residues: 4180 helix: 1.94 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.26 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 52 TYR 0.020 0.003 TYR s 10 PHE 0.013 0.001 PHE d 75 TRP 0.005 0.001 TRP 7 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (32175) covalent geometry : angle 0.59649 / 0.29 (43670) hydrogen bonds : bond 0.03273 / 2.20 ( 2365) hydrogen bonds : angle 3.64917 / 2.43 ( 7095) link_TRANS : bond 0.00267 / 0.18 ( 55) link_TRANS : angle 0.90689 / 0.65 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 645 time to evaluate : 0.991 Fit side-chains REVERT: c 68 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8345 (tp40) REVERT: B 11 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: B 25 VAL cc_start: 0.7983 (t) cc_final: 0.7739 (t) REVERT: G 11 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: H 68 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8156 (tp40) REVERT: I 61 MET cc_start: 0.8657 (mmp) cc_final: 0.8434 (mmt) REVERT: J 7 SER cc_start: 0.8999 (m) cc_final: 0.8589 (t) REVERT: L 68 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8374 (tp40) REVERT: M 2 GLU cc_start: 0.7923 (tt0) cc_final: 0.7611 (tt0) REVERT: Q 2 GLU cc_start: 0.7695 (tt0) cc_final: 0.6979 (mp0) REVERT: R 61 MET cc_start: 0.8550 (mmp) cc_final: 0.8256 (mmm) REVERT: S 61 MET cc_start: 0.8576 (mmp) cc_final: 0.8169 (mmp) REVERT: Z 61 MET cc_start: 0.8809 (mmp) cc_final: 0.8269 (mmm) REVERT: 0 31 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7817 (tt) REVERT: 1 71 MET cc_start: 0.8519 (mmm) cc_final: 0.8042 (mmm) REVERT: 2 71 MET cc_start: 0.8536 (mmm) cc_final: 0.8218 (mmm) REVERT: 3 69 ASN cc_start: 0.8781 (t0) cc_final: 0.8549 (t0) REVERT: 5 29 LEU cc_start: 0.8918 (mt) cc_final: 0.8711 (mt) REVERT: 7 2 GLU cc_start: 0.6864 (tt0) cc_final: 0.6539 (mp0) REVERT: 9 71 MET cc_start: 0.8624 (mmm) cc_final: 0.8400 (mmm) REVERT: a 52 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7889 (ptp-110) REVERT: d 68 GLN cc_start: 0.8653 (tp-100) cc_final: 0.7830 (tp40) REVERT: e 1 SER cc_start: 0.8019 (p) cc_final: 0.7591 (p) REVERT: e 2 GLU cc_start: 0.7942 (tt0) cc_final: 0.7426 (mp0) REVERT: e 71 MET cc_start: 0.8689 (mmm) cc_final: 0.8477 (mmp) REVERT: f 61 MET cc_start: 0.8720 (mmp) cc_final: 0.8322 (mmm) REVERT: f 69 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7707 (t0) REVERT: g 61 MET cc_start: 0.8416 (mmp) cc_final: 0.8114 (mmm) REVERT: i 2 GLU cc_start: 0.7365 (tt0) cc_final: 0.6979 (mp0) REVERT: i 12 SER cc_start: 0.7444 (t) cc_final: 0.7173 (m) REVERT: i 31 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7812 (tp) REVERT: k 55 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (mp) REVERT: l 71 MET cc_start: 0.8547 (mmm) cc_final: 0.8152 (mmm) REVERT: n 2 GLU cc_start: 0.7368 (tt0) cc_final: 0.6897 (mp0) REVERT: n 68 GLN cc_start: 0.8405 (tp40) cc_final: 0.7935 (tp40) REVERT: o 61 MET cc_start: 0.8387 (mmm) cc_final: 0.8123 (mmm) REVERT: o 69 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7578 (t0) REVERT: o 71 MET cc_start: 0.8613 (mmm) cc_final: 0.8376 (mmm) REVERT: p 11 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7581 (mt-10) REVERT: q 11 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: q 18 ARG cc_start: 0.6941 (mtm110) cc_final: 0.4598 (mmt180) REVERT: q 31 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8306 (tp) REVERT: q 59 LEU cc_start: 0.8936 (mt) cc_final: 0.8689 (mt) REVERT: r 69 ASN cc_start: 0.8528 (t0) cc_final: 0.8310 (t0) outliers start: 137 outliers final: 42 residues processed: 747 average time/residue: 0.4441 time to fit residues: 423.2511 Evaluate side-chains 567 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 516 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 36 VAL Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 36 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 3 residue 36 VAL Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 72 SER Chi-restraints excluded: chain 5 residue 36 VAL Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 69 ASN Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 41 LEU Chi-restraints excluded: chain i residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 55 ILE Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain o residue 69 ASN Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain q residue 11 GLU Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain r residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 368 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 357 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 308 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 ASN C 69 ASN M 69 ASN P 69 ASN U 69 ASN V 69 ASN 2 19 ASN 7 69 ASN ** 9 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 ASN s 69 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076629 restraints weight = 53919.087| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.00 r_work: 0.2905 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 32230 Z= 0.224 Angle : 0.627 10.974 43835 Z= 0.319 Chirality : 0.043 0.155 5280 Planarity : 0.004 0.036 5445 Dihedral : 3.927 40.911 4457 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 3.48 % Allowed : 23.82 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.13), residues: 4180 helix: 1.69 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 77 TYR 0.015 0.003 TYR A 10 PHE 0.020 0.002 PHE f 51 TRP 0.007 0.001 TRP p 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.22 (32175) covalent geometry : angle 0.62466 / 0.32 (43670) hydrogen bonds : bond 0.04342 / 2.94 ( 2365) hydrogen bonds : angle 3.65911 / 2.44 ( 7095) link_TRANS : bond 0.00166 / 0.11 ( 55) link_TRANS : angle 1.11495 / 0.77 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 491 time to evaluate : 1.190 Fit side-chains REVERT: c 71 MET cc_start: 0.8931 (mmm) cc_final: 0.8708 (mmt) REVERT: A 11 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7501 (mm-30) REVERT: D 72 SER cc_start: 0.8728 (t) cc_final: 0.8497 (p) REVERT: E 69 ASN cc_start: 0.8654 (t0) cc_final: 0.8440 (t0) REVERT: F 11 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: G 11 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: G 32 ILE cc_start: 0.9104 (mt) cc_final: 0.8893 (mt) REVERT: H 70 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8738 (p) REVERT: K 2 GLU cc_start: 0.7835 (tt0) cc_final: 0.7480 (tt0) REVERT: K 11 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: L 68 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8401 (tp40) REVERT: N 12 SER cc_start: 0.7831 (t) cc_final: 0.7583 (m) REVERT: P 2 GLU cc_start: 0.8044 (tt0) cc_final: 0.7844 (tt0) REVERT: Q 2 GLU cc_start: 0.8274 (tt0) cc_final: 0.8006 (tt0) REVERT: R 69 ASN cc_start: 0.8558 (t0) cc_final: 0.8280 (t0) REVERT: R 71 MET cc_start: 0.8961 (mmm) cc_final: 0.8512 (mmm) REVERT: S 61 MET cc_start: 0.8702 (mmp) cc_final: 0.8482 (mmp) REVERT: S 69 ASN cc_start: 0.8670 (t0) cc_final: 0.8440 (t0) REVERT: T 2 GLU cc_start: 0.7861 (tt0) cc_final: 0.7637 (tt0) REVERT: T 11 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: U 11 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: X 61 MET cc_start: 0.9083 (mmt) cc_final: 0.8776 (mmm) REVERT: Z 2 GLU cc_start: 0.8410 (tt0) cc_final: 0.8097 (tt0) REVERT: Z 20 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8807 (p) REVERT: Z 61 MET cc_start: 0.8945 (mmp) cc_final: 0.8472 (mmm) REVERT: 1 71 MET cc_start: 0.8954 (mmm) cc_final: 0.8692 (mmm) REVERT: 2 61 MET cc_start: 0.8981 (mmt) cc_final: 0.8496 (tpp) REVERT: 2 73 THR cc_start: 0.9172 (p) cc_final: 0.8943 (p) REVERT: 3 52 ARG cc_start: 0.8644 (ttp80) cc_final: 0.8395 (ttp-110) REVERT: 3 69 ASN cc_start: 0.8813 (t0) cc_final: 0.8565 (t0) REVERT: 5 2 GLU cc_start: 0.8021 (tt0) cc_final: 0.6911 (mp0) REVERT: 6 11 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: 7 11 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: 8 20 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8567 (p) REVERT: 9 71 MET cc_start: 0.8836 (mmm) cc_final: 0.8293 (mmm) REVERT: d 71 MET cc_start: 0.8772 (mmm) cc_final: 0.8395 (mmm) REVERT: e 2 GLU cc_start: 0.8130 (tt0) cc_final: 0.7784 (tt0) REVERT: g 2 GLU cc_start: 0.7778 (tt0) cc_final: 0.6999 (mp0) REVERT: g 61 MET cc_start: 0.8708 (mmp) cc_final: 0.8418 (mmm) REVERT: i 11 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: j 55 ILE cc_start: 0.8839 (mm) cc_final: 0.8619 (mp) REVERT: n 2 GLU cc_start: 0.7813 (tt0) cc_final: 0.7097 (mp0) REVERT: n 11 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7516 (mt-10) REVERT: o 61 MET cc_start: 0.8861 (mmm) cc_final: 0.8617 (mmp) REVERT: o 71 MET cc_start: 0.8955 (mmm) cc_final: 0.8600 (mmp) REVERT: p 61 MET cc_start: 0.8864 (mmt) cc_final: 0.8354 (mmm) REVERT: q 31 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8397 (tp) REVERT: s 61 MET cc_start: 0.9057 (mmt) cc_final: 0.8853 (mmt) REVERT: s 68 GLN cc_start: 0.8828 (tp40) cc_final: 0.8623 (tp40) outliers start: 115 outliers final: 50 residues processed: 582 average time/residue: 0.5595 time to fit residues: 397.9492 Evaluate side-chains 444 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 381 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain M residue 72 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 3 residue 12 SER Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 11 GLU Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 22 THR Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain a residue 7 SER Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 7 SER Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 11 GLU Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 22 THR Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain s residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 146 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 339 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 69 ASN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN T 69 ASN U 68 GLN U 69 ASN V 68 GLN ** W 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 69 ASN 5 69 ASN ** 9 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 69 ASN h 69 ASN j 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.082900 restraints weight = 52622.281| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.02 r_work: 0.3008 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32230 Z= 0.120 Angle : 0.551 11.658 43835 Z= 0.276 Chirality : 0.037 0.133 5280 Planarity : 0.005 0.056 5445 Dihedral : 3.630 41.096 4457 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 2.64 % Allowed : 24.79 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.13), residues: 4180 helix: 2.01 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.05 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 0 77 TYR 0.016 0.003 TYR 4 10 PHE 0.011 0.001 PHE l 51 TRP 0.004 0.000 TRP I 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (32175) covalent geometry : angle 0.55114 / 0.28 (43670) hydrogen bonds : bond 0.03368 / 2.28 ( 2365) hydrogen bonds : angle 3.60018 / 2.40 ( 7095) link_TRANS : bond 0.00299 / 0.20 ( 55) link_TRANS : angle 0.42458 / 0.29 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 448 time to evaluate : 1.156 Fit side-chains REVERT: A 11 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: F 11 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: G 11 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: H 70 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8711 (p) REVERT: I 61 MET cc_start: 0.8772 (mmp) cc_final: 0.8491 (mmt) REVERT: L 68 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8324 (tp40) REVERT: P 61 MET cc_start: 0.8764 (mmm) cc_final: 0.8478 (mmp) REVERT: R 71 MET cc_start: 0.8914 (mmm) cc_final: 0.8488 (mmm) REVERT: S 61 MET cc_start: 0.8615 (mmp) cc_final: 0.8346 (mmp) REVERT: U 11 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: Z 55 ILE cc_start: 0.8868 (mm) cc_final: 0.8659 (mm) REVERT: Z 61 MET cc_start: 0.8877 (mmp) cc_final: 0.8371 (mmm) REVERT: 0 12 SER cc_start: 0.7661 (t) cc_final: 0.7407 (m) REVERT: 1 61 MET cc_start: 0.8768 (mmt) cc_final: 0.8372 (mmt) REVERT: 1 71 MET cc_start: 0.8969 (mmm) cc_final: 0.8763 (mmp) REVERT: 2 61 MET cc_start: 0.8990 (mmt) cc_final: 0.8473 (tpp) REVERT: 3 52 ARG cc_start: 0.8298 (ttp80) cc_final: 0.8053 (ttp-110) REVERT: 3 55 ILE cc_start: 0.8641 (mm) cc_final: 0.8421 (mp) REVERT: 4 61 MET cc_start: 0.8778 (mmm) cc_final: 0.8430 (mmt) REVERT: 4 69 ASN cc_start: 0.8617 (t0) cc_final: 0.8374 (t0) REVERT: 8 31 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.8023 (tp) REVERT: 8 61 MET cc_start: 0.8931 (tpp) cc_final: 0.8504 (tpp) REVERT: 8 68 GLN cc_start: 0.8629 (tp40) cc_final: 0.8361 (tp40) REVERT: 9 71 MET cc_start: 0.8753 (mmm) cc_final: 0.8161 (mmm) REVERT: d 71 MET cc_start: 0.8669 (mmm) cc_final: 0.8271 (mmm) REVERT: g 2 GLU cc_start: 0.7526 (tt0) cc_final: 0.6794 (mp0) REVERT: i 11 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: k 55 ILE cc_start: 0.8741 (mm) cc_final: 0.8485 (mp) REVERT: q 31 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (tp) REVERT: s 60 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8488 (p) REVERT: s 61 MET cc_start: 0.8996 (mmt) cc_final: 0.8775 (mmt) outliers start: 87 outliers final: 34 residues processed: 522 average time/residue: 0.4759 time to fit residues: 308.6285 Evaluate side-chains 425 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 382 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 1 residue 7 SER Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain a residue 7 SER Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 11 GLU Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 53 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 329 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 353 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 69 ASN P 69 ASN Q 69 ASN R 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN Z 69 ASN 3 69 ASN 5 69 ASN 9 19 ASN 9 69 ASN b 16 ASN g 69 ASN h 16 ASN h 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.091753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081658 restraints weight = 52462.383| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.94 r_work: 0.2980 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32230 Z= 0.165 Angle : 0.566 8.762 43835 Z= 0.289 Chirality : 0.039 0.139 5280 Planarity : 0.004 0.043 5445 Dihedral : 3.662 42.729 4457 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.85 % Favored : 95.91 % Rotamer: Outliers : 2.94 % Allowed : 24.24 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.13), residues: 4180 helix: 1.90 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.014 0.003 TYR 4 10 PHE 0.016 0.002 PHE F 51 TRP 0.003 0.001 TRP Y 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (32175) covalent geometry : angle 0.56622 / 0.29 (43670) hydrogen bonds : bond 0.03812 / 2.58 ( 2365) hydrogen bonds : angle 3.55111 / 2.37 ( 7095) link_TRANS : bond 0.00146 / 0.10 ( 55) link_TRANS : angle 0.62970 / 0.43 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 408 time to evaluate : 1.105 Fit side-chains REVERT: c 69 ASN cc_start: 0.8903 (t0) cc_final: 0.8698 (t0) REVERT: A 11 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: D 2 GLU cc_start: 0.8153 (tt0) cc_final: 0.7671 (tm-30) REVERT: F 11 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: G 11 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: H 70 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8836 (p) REVERT: I 61 MET cc_start: 0.8865 (mmp) cc_final: 0.8602 (mmt) REVERT: R 71 MET cc_start: 0.9006 (mmm) cc_final: 0.8498 (mmm) REVERT: S 61 MET cc_start: 0.8697 (mmt) cc_final: 0.8493 (mmp) REVERT: T 55 ILE cc_start: 0.8830 (mm) cc_final: 0.8628 (mp) REVERT: U 11 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: V 68 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8329 (tp40) REVERT: Y 77 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7674 (tpt-90) REVERT: Z 55 ILE cc_start: 0.9014 (mm) cc_final: 0.8797 (mm) REVERT: Z 72 SER cc_start: 0.8215 (p) cc_final: 0.7980 (p) REVERT: 0 12 SER cc_start: 0.7859 (t) cc_final: 0.7596 (m) REVERT: 1 7 SER cc_start: 0.9052 (m) cc_final: 0.8787 (m) REVERT: 1 71 MET cc_start: 0.8991 (mmm) cc_final: 0.8753 (mmp) REVERT: 2 61 MET cc_start: 0.9057 (mmt) cc_final: 0.8642 (tpp) REVERT: 3 52 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8326 (ttp-110) REVERT: 8 20 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8531 (p) REVERT: 8 68 GLN cc_start: 0.8796 (tp40) cc_final: 0.8458 (tp40) REVERT: 9 71 MET cc_start: 0.8780 (mmm) cc_final: 0.8134 (mmm) REVERT: b 11 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: d 71 MET cc_start: 0.8884 (mmm) cc_final: 0.8606 (mmm) REVERT: e 69 ASN cc_start: 0.8447 (t0) cc_final: 0.8165 (t0) REVERT: i 11 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: k 55 ILE cc_start: 0.8899 (mm) cc_final: 0.8645 (mp) REVERT: o 61 MET cc_start: 0.8792 (mmm) cc_final: 0.8513 (mmm) REVERT: q 31 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8068 (tp) REVERT: s 60 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (p) REVERT: s 61 MET cc_start: 0.9059 (mmt) cc_final: 0.8672 (tpp) outliers start: 97 outliers final: 43 residues processed: 497 average time/residue: 0.5061 time to fit residues: 311.0360 Evaluate side-chains 430 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain X residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 11 GLU Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 87 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 69 ASN E 69 ASN L 69 ASN P 69 ASN Q 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN Z 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN g 69 ASN h 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077855 restraints weight = 52965.519| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.93 r_work: 0.2919 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 32230 Z= 0.250 Angle : 0.629 9.333 43835 Z= 0.321 Chirality : 0.043 0.152 5280 Planarity : 0.004 0.031 5445 Dihedral : 3.965 43.724 4457 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.46 % Favored : 97.18 % Rotamer: Outliers : 3.36 % Allowed : 23.27 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4180 helix: 1.58 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.12 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG q 77 TYR 0.014 0.003 TYR T 10 PHE 0.019 0.002 PHE 5 51 TRP 0.004 0.001 TRP Y 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.25 (32175) covalent geometry : angle 0.62916 / 0.32 (43670) hydrogen bonds : bond 0.04320 / 2.92 ( 2365) hydrogen bonds : angle 3.71533 / 2.48 ( 7095) link_TRANS : bond 0.00159 / 0.11 ( 55) link_TRANS : angle 0.65021 / 0.47 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 374 time to evaluate : 1.026 Fit side-chains REVERT: A 11 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: F 11 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: G 11 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: H 70 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8826 (p) REVERT: K 11 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: N 61 MET cc_start: 0.9032 (mmt) cc_final: 0.8789 (mmp) REVERT: P 11 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.6974 (mm-30) REVERT: R 60 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8657 (p) REVERT: R 71 MET cc_start: 0.9052 (mmm) cc_final: 0.8557 (mmm) REVERT: S 61 MET cc_start: 0.8746 (mmt) cc_final: 0.8543 (mmp) REVERT: U 11 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: Z 55 ILE cc_start: 0.9028 (mm) cc_final: 0.8804 (mm) REVERT: Z 72 SER cc_start: 0.8328 (p) cc_final: 0.8105 (p) REVERT: 0 12 SER cc_start: 0.7907 (t) cc_final: 0.7612 (m) REVERT: 1 7 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8926 (m) REVERT: 1 71 MET cc_start: 0.8993 (mmm) cc_final: 0.8766 (mmp) REVERT: 2 61 MET cc_start: 0.9056 (mmt) cc_final: 0.8604 (tpp) REVERT: 7 11 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7252 (mt-10) REVERT: 8 20 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8503 (p) REVERT: 8 68 GLN cc_start: 0.8812 (tp40) cc_final: 0.8471 (tp40) REVERT: 9 71 MET cc_start: 0.8821 (mmm) cc_final: 0.8116 (mmm) REVERT: b 11 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7172 (mm-30) REVERT: d 42 ILE cc_start: 0.8686 (tp) cc_final: 0.8470 (tp) REVERT: d 71 MET cc_start: 0.8920 (mmm) cc_final: 0.8666 (mmm) REVERT: e 1 SER cc_start: 0.8032 (p) cc_final: 0.7760 (p) REVERT: e 55 ILE cc_start: 0.8674 (mm) cc_final: 0.8392 (mp) REVERT: h 11 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: i 11 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: k 55 ILE cc_start: 0.8950 (mm) cc_final: 0.8697 (mp) REVERT: l 11 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: o 61 MET cc_start: 0.8877 (mmm) cc_final: 0.8471 (mmm) REVERT: q 31 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8333 (tp) REVERT: s 60 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8689 (p) REVERT: s 61 MET cc_start: 0.9081 (mmt) cc_final: 0.8683 (tpp) outliers start: 111 outliers final: 65 residues processed: 471 average time/residue: 0.4925 time to fit residues: 289.2885 Evaluate side-chains 436 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 31 ILE Chi-restraints excluded: chain c residue 53 THR Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 1 residue 7 SER Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 3 residue 12 SER Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 11 GLU Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 22 THR Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 11 GLU Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 11 GLU Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 11 GLU Chi-restraints excluded: chain i residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 11 GLU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 53 THR Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 22 THR Chi-restraints excluded: chain r residue 31 ILE Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 373 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 318 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 69 ASN H 69 ASN ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 69 ASN R 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN X 69 ASN Z 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN g 69 ASN h 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085062 restraints weight = 52124.052| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.96 r_work: 0.3034 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32230 Z= 0.118 Angle : 0.551 9.244 43835 Z= 0.277 Chirality : 0.037 0.142 5280 Planarity : 0.004 0.053 5445 Dihedral : 3.592 41.674 4457 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 2.18 % Favored : 97.34 % Rotamer: Outliers : 2.58 % Allowed : 24.18 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.14), residues: 4180 helix: 1.95 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.07 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 77 TYR 0.015 0.003 TYR T 10 PHE 0.011 0.001 PHE d 50 TRP 0.005 0.000 TRP 7 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (32175) covalent geometry : angle 0.55161 / 0.28 (43670) hydrogen bonds : bond 0.03406 / 2.29 ( 2365) hydrogen bonds : angle 3.60643 / 2.40 ( 7095) link_TRANS : bond 0.00242 / 0.16 ( 55) link_TRANS : angle 0.31631 / 0.21 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 413 time to evaluate : 1.127 Fit side-chains REVERT: A 11 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: F 11 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: G 11 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: H 70 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8814 (p) REVERT: K 11 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: P 2 GLU cc_start: 0.7795 (tt0) cc_final: 0.7594 (tt0) REVERT: P 11 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6929 (mm-30) REVERT: Q 55 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8725 (mp) REVERT: R 71 MET cc_start: 0.9023 (mmm) cc_final: 0.8567 (mmm) REVERT: S 61 MET cc_start: 0.8657 (mmt) cc_final: 0.8429 (mmp) REVERT: U 11 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: Z 72 SER cc_start: 0.8177 (p) cc_final: 0.7932 (p) REVERT: 1 7 SER cc_start: 0.8980 (m) cc_final: 0.8741 (m) REVERT: 2 61 MET cc_start: 0.8968 (mmt) cc_final: 0.8470 (tpp) REVERT: 3 52 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8207 (ttp-110) REVERT: 8 2 GLU cc_start: 0.7941 (tt0) cc_final: 0.7654 (tt0) REVERT: 8 31 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8082 (tp) REVERT: 8 61 MET cc_start: 0.9014 (tpp) cc_final: 0.8649 (tpp) REVERT: 8 68 GLN cc_start: 0.8765 (tp40) cc_final: 0.8416 (tp40) REVERT: 9 71 MET cc_start: 0.8798 (mmm) cc_final: 0.8208 (mmm) REVERT: d 42 ILE cc_start: 0.8575 (tp) cc_final: 0.8362 (tp) REVERT: d 71 MET cc_start: 0.8855 (mmm) cc_final: 0.8634 (mmm) REVERT: e 69 ASN cc_start: 0.8419 (t0) cc_final: 0.8133 (t0) REVERT: i 22 THR cc_start: 0.8606 (m) cc_final: 0.8217 (p) REVERT: k 55 ILE cc_start: 0.8860 (mm) cc_final: 0.8579 (mp) REVERT: q 31 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7904 (tp) REVERT: r 22 THR cc_start: 0.8719 (m) cc_final: 0.8324 (p) REVERT: s 60 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8571 (p) REVERT: s 61 MET cc_start: 0.9082 (mmt) cc_final: 0.8849 (mmt) outliers start: 85 outliers final: 45 residues processed: 492 average time/residue: 0.5120 time to fit residues: 312.4320 Evaluate side-chains 444 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 388 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 294 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 379 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 219 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 357 optimal weight: 10.0000 chunk 84 optimal weight: 0.0040 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 69 ASN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN U 69 ASN V 69 ASN W 69 ASN Z 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN g 69 ASN h 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.089501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079404 restraints weight = 52899.192| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.93 r_work: 0.2940 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 32230 Z= 0.214 Angle : 0.612 9.242 43835 Z= 0.312 Chirality : 0.041 0.154 5280 Planarity : 0.004 0.039 5445 Dihedral : 3.756 13.107 4455 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.33 % Favored : 96.10 % Rotamer: Outliers : 2.73 % Allowed : 23.85 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.13), residues: 4180 helix: 1.70 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.13 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 77 TYR 0.014 0.003 TYR T 10 PHE 0.017 0.002 PHE l 51 TRP 0.004 0.001 TRP n 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.21 (32175) covalent geometry : angle 0.61155 / 0.31 (43670) hydrogen bonds : bond 0.04125 / 2.78 ( 2365) hydrogen bonds : angle 3.65993 / 2.44 ( 7095) link_TRANS : bond 0.00138 / 0.09 ( 55) link_TRANS : angle 0.61647 / 0.44 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 374 time to evaluate : 1.038 Fit side-chains REVERT: A 11 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: D 2 GLU cc_start: 0.8229 (tt0) cc_final: 0.7708 (tm-30) REVERT: F 11 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: G 11 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7052 (mm-30) REVERT: H 70 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (p) REVERT: I 61 MET cc_start: 0.8952 (mmt) cc_final: 0.8630 (mmt) REVERT: K 11 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7294 (mm-30) REVERT: P 11 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: Q 55 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8725 (mp) REVERT: R 60 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8678 (p) REVERT: R 71 MET cc_start: 0.8985 (mmm) cc_final: 0.8522 (mmm) REVERT: S 61 MET cc_start: 0.8771 (mmt) cc_final: 0.8562 (mmp) REVERT: U 11 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: Z 61 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8668 (tpp) REVERT: Z 72 SER cc_start: 0.8282 (p) cc_final: 0.8050 (p) REVERT: 0 12 SER cc_start: 0.7878 (t) cc_final: 0.7606 (m) REVERT: 1 7 SER cc_start: 0.9147 (m) cc_final: 0.8893 (m) REVERT: 2 61 MET cc_start: 0.9011 (mmt) cc_final: 0.8546 (tpp) REVERT: 6 11 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: 8 20 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (p) REVERT: 9 71 MET cc_start: 0.8845 (mmm) cc_final: 0.8155 (mmm) REVERT: d 71 MET cc_start: 0.8948 (mmm) cc_final: 0.8727 (mmm) REVERT: e 69 ASN cc_start: 0.8474 (t0) cc_final: 0.8192 (t0) REVERT: k 55 ILE cc_start: 0.8933 (mm) cc_final: 0.8687 (mp) REVERT: l 11 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: q 31 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8244 (tp) REVERT: s 60 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (p) outliers start: 90 outliers final: 52 residues processed: 458 average time/residue: 0.4792 time to fit residues: 273.9022 Evaluate side-chains 425 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 358 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain Q residue 31 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 61 MET Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 2 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 22 THR Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 11 GLU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 31 ILE Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain q residue 69 ASN Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 284 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 374 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 69 ASN L 69 ASN P 69 ASN Q 69 ASN R 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN Z 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN 7 69 ASN 8 68 GLN g 69 ASN ** h 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 69 ASN p 69 ASN s 69 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.094574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084503 restraints weight = 51923.069| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.00 r_work: 0.3028 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32230 Z= 0.123 Angle : 0.561 8.849 43835 Z= 0.283 Chirality : 0.037 0.148 5280 Planarity : 0.004 0.049 5445 Dihedral : 3.542 11.536 4455 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.67 % Allowed : 1.96 % Favored : 97.37 % Rotamer: Outliers : 2.21 % Allowed : 24.67 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 4180 helix: 1.94 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.08 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 77 TYR 0.015 0.003 TYR T 10 PHE 0.011 0.001 PHE l 51 TRP 0.006 0.000 TRP 7 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32175) covalent geometry : angle 0.56131 / 0.28 (43670) hydrogen bonds : bond 0.03414 / 2.30 ( 2365) hydrogen bonds : angle 3.61511 / 2.41 ( 7095) link_TRANS : bond 0.00232 / 0.16 ( 55) link_TRANS : angle 0.31186 / 0.21 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 421 time to evaluate : 1.073 Fit side-chains REVERT: c 11 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7125 (mm-30) REVERT: A 11 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: D 2 GLU cc_start: 0.8118 (tt0) cc_final: 0.7623 (tm-30) REVERT: F 11 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: G 11 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: H 70 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8828 (p) REVERT: I 61 MET cc_start: 0.8913 (mmt) cc_final: 0.8685 (mmt) REVERT: K 11 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: P 11 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: Q 55 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8702 (mp) REVERT: R 60 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8669 (p) REVERT: R 71 MET cc_start: 0.9029 (mmm) cc_final: 0.8654 (mmm) REVERT: S 61 MET cc_start: 0.8696 (mmt) cc_final: 0.8459 (mmp) REVERT: U 11 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: V 68 GLN cc_start: 0.8592 (tp-100) cc_final: 0.8281 (tp40) REVERT: Z 72 SER cc_start: 0.8191 (p) cc_final: 0.7930 (p) REVERT: 1 7 SER cc_start: 0.8958 (m) cc_final: 0.8737 (m) REVERT: 2 61 MET cc_start: 0.8990 (mmt) cc_final: 0.8496 (tpp) REVERT: 3 52 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8231 (ttp-110) REVERT: 6 11 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.6952 (mm-30) REVERT: 8 2 GLU cc_start: 0.7947 (tt0) cc_final: 0.7603 (tt0) REVERT: 8 20 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8501 (p) REVERT: 8 31 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8095 (tp) REVERT: 8 61 MET cc_start: 0.9022 (tpp) cc_final: 0.8681 (tpp) REVERT: 9 71 MET cc_start: 0.8808 (mmm) cc_final: 0.8213 (mmm) REVERT: d 71 MET cc_start: 0.8885 (mmm) cc_final: 0.8668 (mmm) REVERT: e 69 ASN cc_start: 0.8381 (t0) cc_final: 0.8064 (t0) REVERT: k 55 ILE cc_start: 0.8885 (mm) cc_final: 0.8616 (mp) REVERT: q 31 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7934 (mm) REVERT: r 22 THR cc_start: 0.8725 (m) cc_final: 0.8337 (p) REVERT: s 60 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8570 (p) outliers start: 73 outliers final: 43 residues processed: 489 average time/residue: 0.5041 time to fit residues: 306.0812 Evaluate side-chains 446 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 388 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 11 GLU Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain P residue 11 GLU Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 8 LEU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 31 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain 8 residue 20 SER Chi-restraints excluded: chain 8 residue 31 ILE Chi-restraints excluded: chain 9 residue 31 ILE Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain o residue 53 THR Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 31 ILE Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 141 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 369 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 331 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 69 ASN R 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN ** X 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN 8 68 GLN 9 69 ASN g 69 ASN h 69 ASN n 69 ASN p 69 ASN s 69 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085334 restraints weight = 52141.075| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.99 r_work: 0.3055 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32230 Z= 0.117 Angle : 0.561 8.587 43835 Z= 0.282 Chirality : 0.037 0.148 5280 Planarity : 0.004 0.047 5445 Dihedral : 3.443 11.213 4455 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.81 % Allowed : 2.73 % Favored : 96.46 % Rotamer: Outliers : 1.82 % Allowed : 25.45 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.14), residues: 4180 helix: 2.03 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.11 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG j 77 TYR 0.015 0.003 TYR 4 10 PHE 0.012 0.001 PHE T 51 TRP 0.008 0.000 TRP 7 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (32175) covalent geometry : angle 0.56120 / 0.28 (43670) hydrogen bonds : bond 0.03314 / 2.23 ( 2365) hydrogen bonds : angle 3.53524 / 2.36 ( 7095) link_TRANS : bond 0.00181 / 0.12 ( 55) link_TRANS : angle 0.35151 / 0.24 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8360 Ramachandran restraints generated. 4180 Oldfield, 0 Emsley, 4180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 436 time to evaluate : 1.064 Fit side-chains REVERT: c 11 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 11 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: C 70 VAL cc_start: 0.8931 (p) cc_final: 0.8615 (m) REVERT: D 2 GLU cc_start: 0.8150 (tt0) cc_final: 0.7717 (tm-30) REVERT: D 73 THR cc_start: 0.9215 (m) cc_final: 0.8853 (p) REVERT: F 55 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8578 (mp) REVERT: G 2 GLU cc_start: 0.7910 (tt0) cc_final: 0.7440 (tm-30) REVERT: G 11 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: H 70 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8679 (p) REVERT: I 61 MET cc_start: 0.8859 (mmt) cc_final: 0.8614 (mmt) REVERT: K 2 GLU cc_start: 0.8198 (tt0) cc_final: 0.7723 (tm-30) REVERT: K 11 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: M 72 SER cc_start: 0.8422 (t) cc_final: 0.8203 (m) REVERT: P 61 MET cc_start: 0.8734 (mmm) cc_final: 0.8397 (mmp) REVERT: Q 55 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8690 (mp) REVERT: R 60 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8599 (p) REVERT: R 71 MET cc_start: 0.8933 (mmm) cc_final: 0.8408 (mmm) REVERT: R 77 ARG cc_start: 0.8155 (tpp80) cc_final: 0.6869 (tpt90) REVERT: U 11 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: V 68 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8258 (tp40) REVERT: Z 31 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8347 (tt) REVERT: Z 72 SER cc_start: 0.8096 (p) cc_final: 0.7828 (p) REVERT: 1 7 SER cc_start: 0.8760 (m) cc_final: 0.8559 (m) REVERT: 2 61 MET cc_start: 0.8995 (mmt) cc_final: 0.8535 (tpp) REVERT: 3 52 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8205 (ttp-110) REVERT: 4 61 MET cc_start: 0.8806 (mmm) cc_final: 0.8517 (mmt) REVERT: 6 11 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.6877 (mm-30) REVERT: 8 2 GLU cc_start: 0.7895 (tt0) cc_final: 0.7533 (tt0) REVERT: 8 61 MET cc_start: 0.8979 (tpp) cc_final: 0.8646 (tpp) REVERT: 9 71 MET cc_start: 0.8789 (mmm) cc_final: 0.8237 (mmm) REVERT: k 55 ILE cc_start: 0.8835 (mm) cc_final: 0.8587 (mp) REVERT: p 12 SER cc_start: 0.7981 (t) cc_final: 0.7626 (m) REVERT: r 22 THR cc_start: 0.8562 (m) cc_final: 0.8146 (p) REVERT: s 60 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8362 (p) outliers start: 60 outliers final: 31 residues processed: 489 average time/residue: 0.4694 time to fit residues: 286.3679 Evaluate side-chains 444 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 11 GLU Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain Q residue 55 ILE Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain U residue 11 GLU Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 0 residue 31 ILE Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 5 residue 31 ILE Chi-restraints excluded: chain 6 residue 11 GLU Chi-restraints excluded: chain 6 residue 31 ILE Chi-restraints excluded: chain 7 residue 31 ILE Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 31 ILE Chi-restraints excluded: chain k residue 14 LEU Chi-restraints excluded: chain l residue 31 ILE Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain p residue 31 ILE Chi-restraints excluded: chain p residue 60 VAL Chi-restraints excluded: chain q residue 60 VAL Chi-restraints excluded: chain r residue 20 SER Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 128 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 69 ASN Q 69 ASN T 69 ASN U 69 ASN V 69 ASN W 69 ASN X 69 ASN Z 69 ASN 1 69 ASN 3 69 ASN 4 69 ASN 5 69 ASN 8 68 GLN 9 69 ASN g 69 ASN h 69 ASN n 69 ASN s 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079583 restraints weight = 52725.308| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.94 r_work: 0.2944 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 32230 Z= 0.224 Angle : 0.628 8.867 43835 Z= 0.321 Chirality : 0.042 0.162 5280 Planarity : 0.004 0.040 5445 Dihedral : 3.769 13.088 4455 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.79 % Allowed : 2.25 % Favored : 96.96 % Rotamer: Outliers : 2.00 % Allowed : 25.36 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.13), residues: 4180 helix: 1.71 (0.09), residues: 3135 sheet: None (None), residues: 0 loop : -1.14 (0.21), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG q 77 TYR 0.014 0.003 TYR T 10 PHE 0.018 0.002 PHE 5 51 TRP 0.004 0.001 TRP H 13 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.22 (32175) covalent geometry : angle 0.62824 / 0.32 (43670) hydrogen bonds : bond 0.04178 / 2.81 ( 2365) hydrogen bonds : angle 3.68564 / 2.46 ( 7095) link_TRANS : bond 0.00137 / 0.09 ( 55) link_TRANS : angle 0.46299 / 0.33 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8422.77 seconds wall clock time: 144 minutes 31.79 seconds (8671.79 seconds total)