Starting phenix.real_space_refine on Sat Jul 4 15:36:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsv_22460/07_2026/7jsv_22460.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 205 5.16 5 C 14801 2.51 5 N 3075 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22140 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 491 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'TRANS': 65} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: 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, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o Time building chain proxies: 1.85, per 1000 atoms: 0.08 Number of scatterers: 22140 At special positions: 0 Unit cell: (98.28, 98.28, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 205 16.00 P 41 15.00 O 4018 8.00 N 3075 7.00 C 14801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 921.4 milliseconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4756 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 8 through 10 No H-bonds generated for 'chain 'A' and resid 8 through 10' Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 23 through 45 Processing helix chain 'A' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 10 No H-bonds generated for 'chain 'B' and resid 8 through 10' Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 23 through 45 Processing helix chain 'B' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 23 through 45 Processing helix chain 'C' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 10 No H-bonds generated for 'chain 'D' and resid 8 through 10' Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 23 through 45 Processing helix chain 'D' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE D 53 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 10 No H-bonds generated for 'chain 'E' and resid 8 through 10' Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 23 through 45 Processing helix chain 'E' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 10 No H-bonds generated for 'chain 'F' and resid 8 through 10' Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 23 through 45 Processing helix chain 'F' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE F 53 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 10 No H-bonds generated for 'chain 'G' and resid 8 through 10' Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 23 through 45 Processing helix chain 'G' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 10 No H-bonds generated for 'chain 'H' and resid 8 through 10' Processing helix chain 'H' and resid 11 through 20 Processing helix chain 'H' and resid 23 through 45 Processing helix chain 'H' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 11 through 20 Processing helix chain 'I' and resid 23 through 45 Processing helix chain 'I' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 23 through 45 Processing helix chain 'J' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE J 53 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 10 No H-bonds generated for 'chain 'K' and resid 8 through 10' Processing helix chain 'K' and resid 11 through 20 Processing helix chain 'K' and resid 23 through 45 Processing helix chain 'K' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE K 53 " --> pdb=" O PHE K 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 11 through 20 Processing helix chain 'L' and resid 23 through 45 Processing helix chain 'L' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 10 No H-bonds generated for 'chain 'M' and resid 8 through 10' Processing helix chain 'M' and resid 11 through 20 Processing helix chain 'M' and resid 23 through 45 Processing helix chain 'M' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE M 53 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 10 No H-bonds generated for 'chain 'N' and resid 8 through 10' Processing helix chain 'N' and resid 11 through 20 Processing helix chain 'N' and resid 23 through 45 Processing helix chain 'N' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE N 53 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 10 No H-bonds generated for 'chain 'O' and resid 8 through 10' Processing helix chain 'O' and resid 11 through 20 Processing helix chain 'O' and resid 23 through 45 Processing helix chain 'O' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE O 53 " --> pdb=" O PHE O 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA O 54 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 10 No H-bonds generated for 'chain 'P' and resid 8 through 10' Processing helix chain 'P' and resid 11 through 20 Processing helix chain 'P' and resid 23 through 45 Processing helix chain 'P' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE P 53 " --> pdb=" O PHE P 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA P 54 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 10 No H-bonds generated for 'chain 'Q' and resid 8 through 10' Processing helix chain 'Q' and resid 11 through 20 Processing helix chain 'Q' and resid 23 through 45 Processing helix chain 'Q' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Q 53 " --> pdb=" O PHE Q 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 10 No H-bonds generated for 'chain 'R' and resid 8 through 10' Processing helix chain 'R' and resid 11 through 20 Processing helix chain 'R' and resid 23 through 45 Processing helix chain 'R' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 8 through 10 No H-bonds generated for 'chain 'S' and resid 8 through 10' Processing helix chain 'S' and resid 11 through 20 Processing helix chain 'S' and resid 23 through 45 Processing helix chain 'S' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE S 53 " --> pdb=" O PHE S 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA S 54 " --> pdb=" O LEU S 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 10 No H-bonds generated for 'chain 'T' and resid 8 through 10' Processing helix chain 'T' and resid 11 through 20 Processing helix chain 'T' and resid 23 through 45 Processing helix chain 'T' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE T 53 " --> pdb=" O PHE T 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 54 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 10 No H-bonds generated for 'chain 'U' and resid 8 through 10' Processing helix chain 'U' and resid 11 through 20 Processing helix chain 'U' and resid 23 through 45 Processing helix chain 'U' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE U 53 " --> pdb=" O PHE U 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA U 54 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 10 No H-bonds generated for 'chain 'V' and resid 8 through 10' Processing helix chain 'V' and resid 11 through 20 Processing helix chain 'V' and resid 23 through 45 Processing helix chain 'V' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE V 53 " --> pdb=" O PHE V 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA V 54 " --> pdb=" O LEU V 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 10 No H-bonds generated for 'chain 'W' and resid 8 through 10' Processing helix chain 'W' and resid 11 through 20 Processing helix chain 'W' and resid 23 through 45 Processing helix chain 'W' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE W 53 " --> pdb=" O PHE W 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA W 54 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 10 No H-bonds generated for 'chain 'X' and resid 8 through 10' Processing helix chain 'X' and resid 11 through 20 Processing helix chain 'X' and resid 23 through 45 Processing helix chain 'X' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE X 53 " --> pdb=" O PHE X 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA X 54 " --> pdb=" O LEU X 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 10 No H-bonds generated for 'chain 'Y' and resid 8 through 10' Processing helix chain 'Y' and resid 11 through 20 Processing helix chain 'Y' and resid 23 through 45 Processing helix chain 'Y' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Y 53 " --> pdb=" O PHE Y 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA Y 54 " --> pdb=" O LEU Y 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 10 No H-bonds generated for 'chain 'Z' and resid 8 through 10' Processing helix chain 'Z' and resid 11 through 20 Processing helix chain 'Z' and resid 23 through 45 Processing helix chain 'Z' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE Z 53 " --> pdb=" O PHE Z 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA Z 54 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 8 through 10 No H-bonds generated for 'chain 'a' and resid 8 through 10' Processing helix chain 'a' and resid 11 through 20 Processing helix chain 'a' and resid 23 through 45 Processing helix chain 'a' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE a 53 " --> pdb=" O PHE a 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 10 No H-bonds generated for 'chain 'b' and resid 8 through 10' Processing helix chain 'b' and resid 11 through 20 Processing helix chain 'b' and resid 23 through 45 Processing helix chain 'b' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE b 53 " --> pdb=" O PHE b 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 10 No H-bonds generated for 'chain 'c' and resid 8 through 10' Processing helix chain 'c' and resid 11 through 20 Processing helix chain 'c' and resid 23 through 45 Processing helix chain 'c' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE c 53 " --> pdb=" O PHE c 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA c 54 " --> pdb=" O LEU c 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 10 No H-bonds generated for 'chain 'd' and resid 8 through 10' Processing helix chain 'd' and resid 11 through 20 Processing helix chain 'd' and resid 23 through 45 Processing helix chain 'd' and resid 47 through 68 removed outlier: 4.468A pdb=" N PHE d 53 " --> pdb=" O PHE d 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA d 54 " --> pdb=" O LEU d 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 10 No H-bonds generated for 'chain 'e' and resid 8 through 10' Processing helix chain 'e' and resid 11 through 20 Processing helix chain 'e' and resid 23 through 45 Processing helix chain 'e' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE e 53 " --> pdb=" O PHE e 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 10 No H-bonds generated for 'chain 'f' and resid 8 through 10' Processing helix chain 'f' and resid 11 through 20 Processing helix chain 'f' and resid 23 through 45 Processing helix chain 'f' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE f 53 " --> pdb=" O PHE f 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'g' and resid 11 through 20 Processing helix chain 'g' and resid 23 through 45 Processing helix chain 'g' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE g 53 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 10 No H-bonds generated for 'chain 'h' and resid 8 through 10' Processing helix chain 'h' and resid 11 through 20 Processing helix chain 'h' and resid 23 through 45 Processing helix chain 'h' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE h 53 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 10 No H-bonds generated for 'chain 'i' and resid 8 through 10' Processing helix chain 'i' and resid 11 through 20 Processing helix chain 'i' and resid 23 through 45 Processing helix chain 'i' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE i 53 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 10 No H-bonds generated for 'chain 'j' and resid 8 through 10' Processing helix chain 'j' and resid 11 through 20 Processing helix chain 'j' and resid 23 through 45 Processing helix chain 'j' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE j 53 " --> pdb=" O PHE j 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA j 54 " --> pdb=" O LEU j 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 10 No H-bonds generated for 'chain 'k' and resid 8 through 10' Processing helix chain 'k' and resid 11 through 20 Processing helix chain 'k' and resid 23 through 45 Processing helix chain 'k' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE k 53 " --> pdb=" O PHE k 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 10 No H-bonds generated for 'chain 'l' and resid 8 through 10' Processing helix chain 'l' and resid 11 through 20 Processing helix chain 'l' and resid 23 through 45 Processing helix chain 'l' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE l 53 " --> pdb=" O PHE l 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 10 No H-bonds generated for 'chain 'm' and resid 8 through 10' Processing helix chain 'm' and resid 11 through 20 Processing helix chain 'm' and resid 23 through 45 Processing helix chain 'm' and resid 47 through 68 removed outlier: 4.470A pdb=" N PHE m 53 " --> pdb=" O PHE m 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA m 54 " --> pdb=" O LEU m 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 10 No H-bonds generated for 'chain 'n' and resid 8 through 10' Processing helix chain 'n' and resid 11 through 20 Processing helix chain 'n' and resid 23 through 45 Processing helix chain 'n' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE n 53 " --> pdb=" O PHE n 49 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA n 54 " --> pdb=" O LEU n 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 10 No H-bonds generated for 'chain 'o' and resid 8 through 10' Processing helix chain 'o' and resid 11 through 20 Processing helix chain 'o' and resid 23 through 45 Processing helix chain 'o' and resid 47 through 68 removed outlier: 4.469A pdb=" N PHE o 53 " --> pdb=" O PHE o 49 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA o 54 " --> pdb=" O LEU o 50 " (cutoff:3.500A) 1681 hydrogen bonds defined for protein. 5043 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3239 1.30 - 1.43: 5576 1.43 - 1.55: 12956 1.55 - 1.67: 205 1.67 - 1.80: 451 Bond restraints: 22427 Sorted by residual: bond pdb=" CB PHE Z 53 " pdb=" CG PHE Z 53 " ideal model delta sigma weight residual 1.502 1.419 0.083 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE d 53 " pdb=" CG PHE d 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.29e+01 bond pdb=" CB PHE H 53 " pdb=" CG PHE H 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CB PHE n 53 " pdb=" CG PHE n 53 " ideal model delta sigma weight residual 1.502 1.420 0.082 2.30e-02 1.89e+03 1.28e+01 bond pdb=" CD GLU b 33 " pdb=" OE1 GLU b 33 " ideal model delta sigma weight residual 1.249 1.181 0.068 1.90e-02 2.77e+03 1.28e+01 ... (remaining 22422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 25141 2.31 - 4.61: 3287 4.61 - 6.92: 764 6.92 - 9.23: 246 9.23 - 11.53: 287 Bond angle restraints: 29725 Sorted by residual: angle pdb=" N MET l 43 " pdb=" CA MET l 43 " pdb=" C MET l 43 " ideal model delta sigma weight residual 111.07 116.58 -5.51 1.07e+00 8.73e-01 2.65e+01 angle pdb=" N MET E 43 " pdb=" CA MET E 43 " pdb=" C MET E 43 " ideal model delta sigma weight residual 111.07 116.55 -5.48 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET P 43 " pdb=" CA MET P 43 " pdb=" C MET P 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.62e+01 angle pdb=" N MET C 43 " pdb=" CA MET C 43 " pdb=" C MET C 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 angle pdb=" N MET O 43 " pdb=" CA MET O 43 " pdb=" C MET O 43 " ideal model delta sigma weight residual 111.07 116.54 -5.47 1.07e+00 8.73e-01 2.61e+01 ... (remaining 29720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.86: 11374 11.86 - 23.71: 1049 23.71 - 35.57: 369 35.57 - 47.42: 123 47.42 - 59.28: 164 Dihedral angle restraints: 13079 sinusoidal: 5576 harmonic: 7503 Sorted by residual: dihedral pdb=" C THR k 18 " pdb=" N THR k 18 " pdb=" CA THR k 18 " pdb=" CB THR k 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.12e+00 dihedral pdb=" C THR V 18 " pdb=" N THR V 18 " pdb=" CA THR V 18 " pdb=" CB THR V 18 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.11e+00 dihedral pdb=" C THR i 18 " pdb=" N THR i 18 " pdb=" CA THR i 18 " pdb=" CB THR i 18 " ideal model delta harmonic sigma weight residual -122.00 -129.54 7.54 0 2.50e+00 1.60e-01 9.09e+00 ... (remaining 13076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1973 0.077 - 0.154: 1058 0.154 - 0.231: 254 0.231 - 0.308: 77 0.308 - 0.385: 41 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA THR V 18 " pdb=" N THR V 18 " pdb=" C THR V 18 " pdb=" CB THR V 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA THR k 18 " pdb=" N THR k 18 " pdb=" C THR k 18 " pdb=" CB THR k 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA THR B 18 " pdb=" N THR B 18 " pdb=" C THR B 18 " pdb=" CB THR B 18 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 3400 not shown) Planarity restraints: 3321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR k 69 " -0.040 2.00e-02 2.50e+03 8.16e-02 6.66e+01 pdb=" C TYR k 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR k 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR k 69 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR e 69 " 0.040 2.00e-02 2.50e+03 8.15e-02 6.65e+01 pdb=" C TYR e 69 " -0.141 2.00e-02 2.50e+03 pdb=" O TYR e 69 " 0.051 2.00e-02 2.50e+03 pdb=" OXT TYR e 69 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR Y 69 " -0.040 2.00e-02 2.50e+03 8.15e-02 6.64e+01 pdb=" C TYR Y 69 " 0.141 2.00e-02 2.50e+03 pdb=" O TYR Y 69 " -0.051 2.00e-02 2.50e+03 pdb=" OXT TYR Y 69 " -0.050 2.00e-02 2.50e+03 ... (remaining 3318 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8954 2.86 - 3.37: 23340 3.37 - 3.88: 37196 3.88 - 4.39: 46431 4.39 - 4.90: 72058 Nonbonded interactions: 187979 Sorted by model distance: nonbonded pdb=" O2 LHG O 101 " pdb=" O3 LHG O 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG K 101 " pdb=" O3 LHG K 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG V 101 " pdb=" O3 LHG V 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG U 101 " pdb=" O3 LHG U 101 " model vdw 2.348 2.432 nonbonded pdb=" O2 LHG o 101 " pdb=" O3 LHG o 101 " model vdw 2.348 2.432 ... (remaining 187974 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.020 0.083 22427 Z= 1.034 Angle : 2.098 11.533 29725 Z= 1.152 Chirality : 0.103 0.385 3403 Planarity : 0.012 0.082 3321 Dihedral : 13.456 59.276 8323 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 2624 helix: 0.28 (0.09), residues: 2091 sheet: None (None), residues: 0 loop : 3.70 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.011 TYR b 69 PHE 0.019 0.004 PHE b 51 TRP 0.020 0.010 TRP Z 28 Details of bonding type rmsd/Z covalent geometry : bond 0.01953 / 1.03 (22427) covalent geometry : angle 2.09753 / 1.15 (29725) hydrogen bonds : bond 0.16789 / 10.90 ( 1681) hydrogen bonds : angle 7.48958 / 5.22 ( 5043) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 999 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7996 (mmm) cc_final: 0.7758 (tpp) REVERT: A 9 LYS cc_start: 0.8726 (tttt) cc_final: 0.8372 (tttt) REVERT: A 41 TYR cc_start: 0.8508 (t80) cc_final: 0.8181 (t80) REVERT: B 7 LEU cc_start: 0.8962 (mt) cc_final: 0.8566 (mt) REVERT: B 9 LYS cc_start: 0.9005 (tttt) cc_final: 0.8408 (ttpp) REVERT: B 23 SER cc_start: 0.8826 (p) cc_final: 0.8264 (t) REVERT: B 41 TYR cc_start: 0.8907 (t80) cc_final: 0.8545 (t80) REVERT: C 9 LYS cc_start: 0.8420 (tttt) cc_final: 0.7651 (ttpp) REVERT: D 9 LYS cc_start: 0.8851 (tttt) cc_final: 0.7998 (ttpp) REVERT: D 18 THR cc_start: 0.9005 (m) cc_final: 0.8781 (p) REVERT: D 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8516 (t80) REVERT: E 9 LYS cc_start: 0.8519 (tttt) cc_final: 0.8175 (ttpt) REVERT: E 23 SER cc_start: 0.9262 (p) cc_final: 0.8913 (t) REVERT: F 23 SER cc_start: 0.8621 (p) cc_final: 0.8326 (t) REVERT: G 21 LYS cc_start: 0.8117 (tttt) cc_final: 0.7638 (tptt) REVERT: G 23 SER cc_start: 0.9260 (p) cc_final: 0.8949 (p) REVERT: G 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8063 (t80) REVERT: G 64 MET cc_start: 0.8707 (mmt) cc_final: 0.8458 (mmm) REVERT: I 21 LYS cc_start: 0.8205 (tttt) cc_final: 0.7591 (tppt) REVERT: J 42 MET cc_start: 0.9147 (tmm) cc_final: 0.8852 (tmm) REVERT: K 9 LYS cc_start: 0.7983 (tttt) cc_final: 0.7398 (tptt) REVERT: L 9 LYS cc_start: 0.8466 (tttt) cc_final: 0.8170 (ttpt) REVERT: L 65 SER cc_start: 0.9454 (t) cc_final: 0.9059 (p) REVERT: M 9 LYS cc_start: 0.7617 (tttt) cc_final: 0.7055 (ttpt) REVERT: N 9 LYS cc_start: 0.8296 (tttt) cc_final: 0.8045 (ttmt) REVERT: O 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8523 (ttmm) REVERT: O 21 LYS cc_start: 0.7695 (tttt) cc_final: 0.7318 (tptm) REVERT: P 23 SER cc_start: 0.7849 (p) cc_final: 0.7523 (p) REVERT: P 65 SER cc_start: 0.8938 (t) cc_final: 0.8518 (p) REVERT: Q 40 MET cc_start: 0.9117 (mmm) cc_final: 0.8803 (mmt) REVERT: Q 42 MET cc_start: 0.8879 (tmm) cc_final: 0.8483 (tmm) REVERT: R 12 ASP cc_start: 0.7719 (m-30) cc_final: 0.7368 (m-30) REVERT: R 16 LYS cc_start: 0.8682 (tttt) cc_final: 0.8445 (ttpt) REVERT: S 9 LYS cc_start: 0.7838 (tttt) cc_final: 0.7634 (ttpp) REVERT: S 12 ASP cc_start: 0.7659 (m-30) cc_final: 0.7358 (m-30) REVERT: S 46 ASN cc_start: 0.8507 (t0) cc_final: 0.8225 (t0) REVERT: T 9 LYS cc_start: 0.8792 (tttt) cc_final: 0.8572 (tttt) REVERT: T 23 SER cc_start: 0.8875 (p) cc_final: 0.8596 (t) REVERT: U 8 MET cc_start: 0.7231 (mmm) cc_final: 0.6730 (tpp) REVERT: U 9 LYS cc_start: 0.7891 (tttt) cc_final: 0.7679 (ttpp) REVERT: U 41 TYR cc_start: 0.7928 (t80) cc_final: 0.7495 (t80) REVERT: V 39 ILE cc_start: 0.9518 (tp) cc_final: 0.9299 (tp) REVERT: Y 23 SER cc_start: 0.8995 (p) cc_final: 0.8708 (t) REVERT: Y 64 MET cc_start: 0.8349 (mmt) cc_final: 0.7986 (mmm) REVERT: Z 53 PHE cc_start: 0.8513 (t80) cc_final: 0.7744 (t80) REVERT: a 46 ASN cc_start: 0.8863 (t0) cc_final: 0.8568 (t0) REVERT: c 12 ASP cc_start: 0.7717 (m-30) cc_final: 0.7509 (m-30) REVERT: d 8 MET cc_start: 0.7600 (mmm) cc_final: 0.7190 (mmt) REVERT: e 8 MET cc_start: 0.7530 (mmm) cc_final: 0.7330 (mmp) REVERT: f 9 LYS cc_start: 0.8279 (tttt) cc_final: 0.8076 (tppt) REVERT: g 9 LYS cc_start: 0.8460 (tttt) cc_final: 0.8156 (ptmt) REVERT: h 50 LEU cc_start: 0.9062 (mt) cc_final: 0.8797 (mt) REVERT: i 9 LYS cc_start: 0.8399 (tttt) cc_final: 0.7801 (tptt) REVERT: i 41 TYR cc_start: 0.8488 (t80) cc_final: 0.8211 (t80) REVERT: i 65 SER cc_start: 0.9180 (t) cc_final: 0.8961 (p) REVERT: j 28 TRP cc_start: 0.8069 (m-10) cc_final: 0.7802 (m-10) REVERT: j 64 MET cc_start: 0.7877 (mmt) cc_final: 0.7584 (mmp) REVERT: k 12 ASP cc_start: 0.8234 (m-30) cc_final: 0.7966 (m-30) REVERT: k 64 MET cc_start: 0.8457 (mmt) cc_final: 0.8236 (mmm) REVERT: l 42 MET cc_start: 0.8857 (tmm) cc_final: 0.8317 (tmm) REVERT: m 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7405 (t80) REVERT: o 49 PHE cc_start: 0.8349 (m-80) cc_final: 0.8113 (m-10) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.1308 time to fit residues: 208.2737 Evaluate side-chains 682 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103665 restraints weight = 29865.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107116 restraints weight = 14419.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109259 restraints weight = 8055.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.110501 restraints weight = 5122.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111359 restraints weight = 3737.955| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22427 Z= 0.211 Angle : 0.689 8.666 29725 Z= 0.368 Chirality : 0.043 0.194 3403 Planarity : 0.004 0.018 3321 Dihedral : 14.527 85.852 4100 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.78 % Allowed : 14.31 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.16), residues: 2624 helix: 1.25 (0.10), residues: 2091 sheet: None (None), residues: 0 loop : 3.80 (0.33), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR R 41 PHE 0.025 0.002 PHE C 49 TRP 0.009 0.001 TRP I 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (22427) covalent geometry : angle 0.68944 / 0.37 (29725) hydrogen bonds : bond 0.05236 / 3.44 ( 1681) hydrogen bonds : angle 5.97639 / 4.18 ( 5043) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 743 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8901 (tttt) cc_final: 0.8674 (tttm) REVERT: A 39 ILE cc_start: 0.9192 (tp) cc_final: 0.8991 (tp) REVERT: B 9 LYS cc_start: 0.9073 (tttt) cc_final: 0.8710 (ttpp) REVERT: C 9 LYS cc_start: 0.8503 (tttt) cc_final: 0.8242 (ttpp) REVERT: C 23 SER cc_start: 0.8337 (t) cc_final: 0.8129 (t) REVERT: D 9 LYS cc_start: 0.8920 (tttt) cc_final: 0.8431 (ttpp) REVERT: E 23 SER cc_start: 0.8628 (p) cc_final: 0.8344 (p) REVERT: F 64 MET cc_start: 0.8436 (mmm) cc_final: 0.8144 (mmm) REVERT: G 21 LYS cc_start: 0.8276 (tttt) cc_final: 0.7751 (tptt) REVERT: G 41 TYR cc_start: 0.8557 (t80) cc_final: 0.8029 (t80) REVERT: G 64 MET cc_start: 0.8915 (mmt) cc_final: 0.8683 (mmm) REVERT: H 8 MET cc_start: 0.7558 (tpp) cc_final: 0.7354 (tpp) REVERT: H 41 TYR cc_start: 0.8750 (t80) cc_final: 0.8235 (t80) REVERT: J 23 SER cc_start: 0.7884 (p) cc_final: 0.7565 (p) REVERT: K 9 LYS cc_start: 0.8546 (tttt) cc_final: 0.8167 (tptt) REVERT: K 21 LYS cc_start: 0.8401 (tttt) cc_final: 0.8167 (tptp) REVERT: L 65 SER cc_start: 0.9351 (t) cc_final: 0.9049 (p) REVERT: M 9 LYS cc_start: 0.8265 (tttt) cc_final: 0.8050 (tptt) REVERT: M 64 MET cc_start: 0.8198 (mmt) cc_final: 0.7954 (mmt) REVERT: N 65 SER cc_start: 0.9170 (t) cc_final: 0.8636 (p) REVERT: P 33 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8562 (tm-30) REVERT: P 41 TYR cc_start: 0.9183 (t80) cc_final: 0.8885 (t80) REVERT: P 65 SER cc_start: 0.8919 (t) cc_final: 0.8415 (p) REVERT: Q 40 MET cc_start: 0.9079 (mmm) cc_final: 0.8612 (mmt) REVERT: R 42 MET cc_start: 0.8997 (tmm) cc_final: 0.8777 (tmm) REVERT: R 64 MET cc_start: 0.8837 (mmm) cc_final: 0.8599 (mmm) REVERT: S 21 LYS cc_start: 0.8570 (tptm) cc_final: 0.8190 (tptm) REVERT: T 40 MET cc_start: 0.8956 (mmm) cc_final: 0.8744 (tpp) REVERT: U 41 TYR cc_start: 0.8646 (t80) cc_final: 0.8381 (t80) REVERT: U 64 MET cc_start: 0.8579 (mmt) cc_final: 0.8369 (mmm) REVERT: U 65 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8821 (p) REVERT: X 8 MET cc_start: 0.7884 (tpp) cc_final: 0.7420 (tpp) REVERT: Y 64 MET cc_start: 0.8641 (mmt) cc_final: 0.8410 (mmm) REVERT: Z 41 TYR cc_start: 0.8961 (t80) cc_final: 0.8537 (t80) REVERT: a 8 MET cc_start: 0.7753 (tpp) cc_final: 0.7519 (tpp) REVERT: c 42 MET cc_start: 0.8650 (tmm) cc_final: 0.8254 (tmm) REVERT: d 15 VAL cc_start: 0.9089 (m) cc_final: 0.8829 (p) REVERT: d 41 TYR cc_start: 0.8912 (t80) cc_final: 0.8702 (t80) REVERT: e 41 TYR cc_start: 0.8864 (t80) cc_final: 0.8622 (t80) REVERT: e 65 SER cc_start: 0.9038 (t) cc_final: 0.8617 (p) REVERT: f 41 TYR cc_start: 0.9191 (t80) cc_final: 0.8969 (t80) REVERT: h 9 LYS cc_start: 0.8143 (tttt) cc_final: 0.7889 (tppt) REVERT: h 50 LEU cc_start: 0.9180 (mt) cc_final: 0.8914 (mt) REVERT: i 9 LYS cc_start: 0.8656 (tttt) cc_final: 0.8390 (tptt) REVERT: i 41 TYR cc_start: 0.8636 (t80) cc_final: 0.8420 (t80) REVERT: j 12 ASP cc_start: 0.8448 (p0) cc_final: 0.8060 (m-30) REVERT: j 39 ILE cc_start: 0.9611 (tp) cc_final: 0.9276 (tp) REVERT: j 42 MET cc_start: 0.9114 (tmm) cc_final: 0.8534 (tmm) REVERT: k 64 MET cc_start: 0.8932 (mmt) cc_final: 0.8665 (mmm) REVERT: l 42 MET cc_start: 0.9197 (tmm) cc_final: 0.8844 (tmm) REVERT: l 50 LEU cc_start: 0.9325 (mt) cc_final: 0.9045 (mt) REVERT: l 56 ILE cc_start: 0.9387 (tp) cc_final: 0.9170 (tp) REVERT: n 40 MET cc_start: 0.8307 (mmp) cc_final: 0.7813 (mmt) REVERT: n 65 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8204 (p) REVERT: o 9 LYS cc_start: 0.8708 (tttt) cc_final: 0.8388 (ttmt) REVERT: o 41 TYR cc_start: 0.8620 (t80) cc_final: 0.8247 (t80) outliers start: 102 outliers final: 59 residues processed: 796 average time/residue: 0.1243 time to fit residues: 161.8471 Evaluate side-chains 685 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 624 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain V residue 29 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 61 THR Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain m residue 61 THR Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 0.0040 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.101634 restraints weight = 29795.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105026 restraints weight = 14168.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107061 restraints weight = 7841.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.108367 restraints weight = 5021.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108999 restraints weight = 3648.496| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22427 Z= 0.165 Angle : 0.618 9.647 29725 Z= 0.321 Chirality : 0.041 0.181 3403 Planarity : 0.003 0.019 3321 Dihedral : 13.329 84.965 4100 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 5.44 % Allowed : 17.35 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.16), residues: 2624 helix: 1.50 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.56 (0.31), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR T 41 PHE 0.018 0.001 PHE C 49 TRP 0.006 0.001 TRP I 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (22427) covalent geometry : angle 0.61764 / 0.32 (29725) hydrogen bonds : bond 0.04720 / 3.10 ( 1681) hydrogen bonds : angle 5.67347 / 3.96 ( 5043) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 635 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7441 (tm-30) REVERT: B 12 ASP cc_start: 0.8704 (m-30) cc_final: 0.8293 (t0) REVERT: B 64 MET cc_start: 0.9029 (mmm) cc_final: 0.8823 (mmm) REVERT: C 23 SER cc_start: 0.8544 (t) cc_final: 0.8258 (t) REVERT: D 9 LYS cc_start: 0.8848 (tttt) cc_final: 0.8417 (ttpp) REVERT: E 23 SER cc_start: 0.8971 (p) cc_final: 0.8685 (p) REVERT: F 64 MET cc_start: 0.8543 (mmm) cc_final: 0.8330 (mmm) REVERT: G 21 LYS cc_start: 0.8326 (tttt) cc_final: 0.7741 (tptt) REVERT: G 23 SER cc_start: 0.8757 (p) cc_final: 0.8465 (p) REVERT: G 41 TYR cc_start: 0.8532 (t80) cc_final: 0.7827 (t80) REVERT: H 41 TYR cc_start: 0.8723 (t80) cc_final: 0.8346 (t80) REVERT: J 8 MET cc_start: 0.7690 (tpp) cc_final: 0.7451 (tpp) REVERT: K 9 LYS cc_start: 0.8603 (tttt) cc_final: 0.8402 (tptt) REVERT: L 41 TYR cc_start: 0.8829 (t80) cc_final: 0.8439 (t80) REVERT: N 48 LYS cc_start: 0.8846 (pttp) cc_final: 0.8643 (pttp) REVERT: N 62 ILE cc_start: 0.8834 (mm) cc_final: 0.8547 (mt) REVERT: N 64 MET cc_start: 0.8844 (mmm) cc_final: 0.8555 (mmm) REVERT: N 65 SER cc_start: 0.9127 (t) cc_final: 0.8749 (p) REVERT: P 41 TYR cc_start: 0.9182 (t80) cc_final: 0.8831 (t80) REVERT: P 62 ILE cc_start: 0.8715 (mm) cc_final: 0.8449 (tp) REVERT: P 65 SER cc_start: 0.8919 (t) cc_final: 0.8673 (p) REVERT: Q 40 MET cc_start: 0.8956 (mmm) cc_final: 0.8565 (mmt) REVERT: T 42 MET cc_start: 0.8663 (ttp) cc_final: 0.8086 (tmm) REVERT: U 65 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8872 (p) REVERT: W 56 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8193 (mt) REVERT: X 46 ASN cc_start: 0.8748 (t0) cc_final: 0.8454 (t0) REVERT: Y 41 TYR cc_start: 0.8887 (t80) cc_final: 0.8683 (t80) REVERT: Y 64 MET cc_start: 0.8522 (mmt) cc_final: 0.8212 (mmm) REVERT: Z 41 TYR cc_start: 0.9049 (t80) cc_final: 0.8504 (t80) REVERT: a 8 MET cc_start: 0.7752 (tpp) cc_final: 0.7509 (tpp) REVERT: a 9 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8681 (ttmm) REVERT: c 64 MET cc_start: 0.8693 (mmt) cc_final: 0.8073 (mmm) REVERT: e 44 THR cc_start: 0.9337 (m) cc_final: 0.9108 (m) REVERT: e 50 LEU cc_start: 0.8718 (mt) cc_final: 0.8207 (mt) REVERT: e 65 SER cc_start: 0.9065 (t) cc_final: 0.8690 (p) REVERT: g 42 MET cc_start: 0.8459 (tmm) cc_final: 0.7163 (tpt) REVERT: h 15 VAL cc_start: 0.9059 (m) cc_final: 0.8664 (p) REVERT: h 21 LYS cc_start: 0.8160 (tttt) cc_final: 0.7737 (tptm) REVERT: h 50 LEU cc_start: 0.9194 (mt) cc_final: 0.8883 (mt) REVERT: j 39 ILE cc_start: 0.9611 (tp) cc_final: 0.9186 (tp) REVERT: j 42 MET cc_start: 0.9075 (tmm) cc_final: 0.8509 (tmm) REVERT: j 56 ILE cc_start: 0.9197 (tt) cc_final: 0.8992 (tt) REVERT: j 64 MET cc_start: 0.7191 (mmp) cc_final: 0.6856 (mmt) REVERT: k 64 MET cc_start: 0.9006 (mmt) cc_final: 0.8590 (mmm) REVERT: l 50 LEU cc_start: 0.9389 (mt) cc_final: 0.9076 (mt) REVERT: n 40 MET cc_start: 0.8364 (mmp) cc_final: 0.7980 (mmt) REVERT: n 65 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8137 (p) REVERT: o 9 LYS cc_start: 0.8679 (tttt) cc_final: 0.8279 (ttpp) REVERT: o 41 TYR cc_start: 0.8566 (t80) cc_final: 0.8249 (t80) outliers start: 116 outliers final: 81 residues processed: 702 average time/residue: 0.1233 time to fit residues: 142.1189 Evaluate side-chains 671 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 586 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 65 SER Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 72 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.0570 chunk 243 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.100124 restraints weight = 30130.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103466 restraints weight = 14327.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105538 restraints weight = 7967.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106740 restraints weight = 5078.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.107552 restraints weight = 3719.632| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22427 Z= 0.172 Angle : 0.618 9.552 29725 Z= 0.318 Chirality : 0.041 0.188 3403 Planarity : 0.003 0.020 3321 Dihedral : 13.005 89.196 4100 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 5.39 % Allowed : 18.34 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.17), residues: 2624 helix: 1.59 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 1.82 (0.34), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR X 41 PHE 0.019 0.001 PHE j 53 TRP 0.006 0.001 TRP I 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (22427) covalent geometry : angle 0.61815 / 0.32 (29725) hydrogen bonds : bond 0.04688 / 3.07 ( 1681) hydrogen bonds : angle 5.51874 / 3.85 ( 5043) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 636 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8679 (m-30) cc_final: 0.8297 (t0) REVERT: B 64 MET cc_start: 0.9076 (mmm) cc_final: 0.8825 (mmm) REVERT: C 23 SER cc_start: 0.8614 (t) cc_final: 0.8243 (t) REVERT: C 41 TYR cc_start: 0.8520 (t80) cc_final: 0.8290 (t80) REVERT: C 64 MET cc_start: 0.9138 (mmt) cc_final: 0.8745 (mmm) REVERT: D 9 LYS cc_start: 0.8894 (tttt) cc_final: 0.8590 (ttpp) REVERT: E 23 SER cc_start: 0.8951 (p) cc_final: 0.8656 (p) REVERT: G 21 LYS cc_start: 0.8357 (tttt) cc_final: 0.8017 (tptt) REVERT: G 23 SER cc_start: 0.8884 (p) cc_final: 0.8563 (p) REVERT: G 41 TYR cc_start: 0.8624 (t80) cc_final: 0.8016 (t80) REVERT: H 41 TYR cc_start: 0.8851 (t80) cc_final: 0.8393 (t80) REVERT: H 42 MET cc_start: 0.9183 (tmm) cc_final: 0.8786 (tmm) REVERT: I 41 TYR cc_start: 0.8667 (t80) cc_final: 0.8387 (t80) REVERT: L 41 TYR cc_start: 0.8844 (t80) cc_final: 0.8455 (t80) REVERT: M 12 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8784 (t0) REVERT: N 8 MET cc_start: 0.7613 (tpp) cc_final: 0.7402 (tpp) REVERT: N 62 ILE cc_start: 0.8897 (mm) cc_final: 0.8663 (mm) REVERT: N 65 SER cc_start: 0.9136 (t) cc_final: 0.8742 (p) REVERT: P 41 TYR cc_start: 0.9060 (t80) cc_final: 0.8685 (t80) REVERT: P 62 ILE cc_start: 0.8748 (mm) cc_final: 0.8390 (mm) REVERT: P 65 SER cc_start: 0.8824 (t) cc_final: 0.8564 (p) REVERT: Q 40 MET cc_start: 0.8932 (mmm) cc_final: 0.8553 (mmt) REVERT: U 41 TYR cc_start: 0.8657 (t80) cc_final: 0.8431 (t80) REVERT: U 64 MET cc_start: 0.8645 (mmt) cc_final: 0.8244 (mmt) REVERT: X 46 ASN cc_start: 0.8849 (t0) cc_final: 0.8585 (t0) REVERT: Y 41 TYR cc_start: 0.8889 (t80) cc_final: 0.8595 (t80) REVERT: Y 64 MET cc_start: 0.8466 (mmt) cc_final: 0.8164 (mmm) REVERT: a 8 MET cc_start: 0.7744 (tpp) cc_final: 0.7467 (tpp) REVERT: b 64 MET cc_start: 0.8277 (mmp) cc_final: 0.7939 (mmp) REVERT: c 9 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8292 (ptmt) REVERT: e 44 THR cc_start: 0.9113 (m) cc_final: 0.8878 (m) REVERT: e 65 SER cc_start: 0.9073 (t) cc_final: 0.8775 (p) REVERT: f 9 LYS cc_start: 0.8572 (tppt) cc_final: 0.8202 (ttmm) REVERT: f 21 LYS cc_start: 0.7800 (tttt) cc_final: 0.7336 (tptm) REVERT: f 43 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7771 (mpp) REVERT: h 15 VAL cc_start: 0.9086 (m) cc_final: 0.8821 (p) REVERT: h 21 LYS cc_start: 0.8246 (tttt) cc_final: 0.7817 (tptm) REVERT: h 50 LEU cc_start: 0.9233 (mt) cc_final: 0.8933 (mt) REVERT: j 39 ILE cc_start: 0.9585 (tp) cc_final: 0.9177 (tp) REVERT: j 42 MET cc_start: 0.9062 (tmm) cc_final: 0.8428 (tmm) REVERT: j 64 MET cc_start: 0.7183 (mmp) cc_final: 0.6758 (mmt) REVERT: k 64 MET cc_start: 0.9011 (mmt) cc_final: 0.8637 (mmm) REVERT: l 42 MET cc_start: 0.9148 (tmm) cc_final: 0.8693 (tmm) REVERT: l 50 LEU cc_start: 0.9396 (mt) cc_final: 0.9088 (mt) REVERT: n 8 MET cc_start: 0.7147 (tpt) cc_final: 0.5653 (ptt) REVERT: n 42 MET cc_start: 0.8424 (tmm) cc_final: 0.7901 (tmm) REVERT: o 9 LYS cc_start: 0.8725 (tttt) cc_final: 0.8280 (ttpp) REVERT: o 41 TYR cc_start: 0.8588 (t80) cc_final: 0.8336 (t80) REVERT: o 64 MET cc_start: 0.8646 (tpp) cc_final: 0.8381 (mmm) outliers start: 115 outliers final: 91 residues processed: 704 average time/residue: 0.1257 time to fit residues: 144.3602 Evaluate side-chains 668 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 574 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 40 MET Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 55 ILE Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 74 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 22 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.120602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104703 restraints weight = 29487.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108133 restraints weight = 13924.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110258 restraints weight = 7694.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111429 restraints weight = 4879.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112240 restraints weight = 3587.805| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22427 Z= 0.129 Angle : 0.598 11.837 29725 Z= 0.299 Chirality : 0.039 0.176 3403 Planarity : 0.002 0.018 3321 Dihedral : 12.524 82.385 4100 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.08 % Allowed : 21.44 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.16), residues: 2624 helix: 1.76 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 1.00 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR c 41 PHE 0.017 0.001 PHE Z 19 TRP 0.006 0.001 TRP Q 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (22427) covalent geometry : angle 0.59755 / 0.30 (29725) hydrogen bonds : bond 0.04014 / 2.64 ( 1681) hydrogen bonds : angle 5.38112 / 3.74 ( 5043) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 630 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.8977 (mmm) cc_final: 0.8736 (mmm) REVERT: C 64 MET cc_start: 0.9066 (mmt) cc_final: 0.8530 (mmm) REVERT: D 9 LYS cc_start: 0.8944 (tttt) cc_final: 0.8648 (ttpp) REVERT: D 64 MET cc_start: 0.9129 (mmm) cc_final: 0.8868 (mmt) REVERT: E 23 SER cc_start: 0.8925 (p) cc_final: 0.8640 (p) REVERT: G 23 SER cc_start: 0.8862 (p) cc_final: 0.8556 (p) REVERT: G 41 TYR cc_start: 0.8506 (t80) cc_final: 0.8039 (t80) REVERT: H 19 PHE cc_start: 0.9111 (m-80) cc_final: 0.8662 (m-10) REVERT: H 41 TYR cc_start: 0.8795 (t80) cc_final: 0.8463 (t80) REVERT: H 42 MET cc_start: 0.9122 (tmm) cc_final: 0.8812 (tmm) REVERT: I 41 TYR cc_start: 0.8659 (t80) cc_final: 0.8263 (t80) REVERT: K 64 MET cc_start: 0.8505 (tpp) cc_final: 0.8126 (mmt) REVERT: M 9 LYS cc_start: 0.8445 (ttpt) cc_final: 0.7928 (tptt) REVERT: M 12 ASP cc_start: 0.9057 (m-30) cc_final: 0.8826 (t0) REVERT: N 62 ILE cc_start: 0.8855 (mm) cc_final: 0.8403 (mm) REVERT: N 65 SER cc_start: 0.9003 (t) cc_final: 0.8707 (p) REVERT: P 41 TYR cc_start: 0.8986 (t80) cc_final: 0.8643 (t80) REVERT: P 62 ILE cc_start: 0.8498 (mm) cc_final: 0.8292 (mm) REVERT: P 64 MET cc_start: 0.8894 (mmm) cc_final: 0.8535 (mmt) REVERT: S 42 MET cc_start: 0.8625 (tmm) cc_final: 0.8315 (tmm) REVERT: U 64 MET cc_start: 0.8722 (mmt) cc_final: 0.8279 (mmt) REVERT: W 41 TYR cc_start: 0.8823 (t80) cc_final: 0.8594 (t80) REVERT: X 46 ASN cc_start: 0.8820 (t0) cc_final: 0.8445 (t0) REVERT: Y 41 TYR cc_start: 0.8777 (t80) cc_final: 0.8344 (t80) REVERT: a 8 MET cc_start: 0.7715 (tpp) cc_final: 0.7345 (tpp) REVERT: a 9 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (ttpt) REVERT: a 41 TYR cc_start: 0.8683 (t80) cc_final: 0.8360 (t80) REVERT: b 64 MET cc_start: 0.8087 (mmp) cc_final: 0.7784 (mmp) REVERT: c 9 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8355 (ptmt) REVERT: c 64 MET cc_start: 0.8663 (mmt) cc_final: 0.8168 (mmm) REVERT: d 8 MET cc_start: 0.7868 (mmm) cc_final: 0.7613 (mmm) REVERT: e 50 LEU cc_start: 0.8645 (mt) cc_final: 0.8225 (mt) REVERT: e 65 SER cc_start: 0.9027 (t) cc_final: 0.8738 (p) REVERT: f 9 LYS cc_start: 0.8657 (tppt) cc_final: 0.8428 (tppt) REVERT: f 21 LYS cc_start: 0.7760 (tttt) cc_final: 0.7309 (tptm) REVERT: f 43 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7746 (mpp) REVERT: h 50 LEU cc_start: 0.9167 (mt) cc_final: 0.8853 (mt) REVERT: i 33 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6753 (tm-30) REVERT: j 39 ILE cc_start: 0.9560 (tp) cc_final: 0.9204 (tp) REVERT: j 42 MET cc_start: 0.9064 (tmm) cc_final: 0.8301 (tmm) REVERT: j 64 MET cc_start: 0.7178 (mmp) cc_final: 0.6785 (mmt) REVERT: k 64 MET cc_start: 0.8977 (mmt) cc_final: 0.8552 (mmm) REVERT: l 42 MET cc_start: 0.9171 (tmm) cc_final: 0.8707 (tmm) REVERT: l 50 LEU cc_start: 0.9337 (mt) cc_final: 0.9052 (mt) REVERT: n 8 MET cc_start: 0.7228 (tpt) cc_final: 0.5764 (ptt) REVERT: o 64 MET cc_start: 0.8578 (tpp) cc_final: 0.8229 (mmm) outliers start: 87 outliers final: 66 residues processed: 682 average time/residue: 0.1246 time to fit residues: 138.9959 Evaluate side-chains 647 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 578 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 40 MET Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 55 ILE Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 23 SER Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 188 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 162 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 89 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.114396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.098324 restraints weight = 30490.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.101539 restraints weight = 14554.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103493 restraints weight = 8205.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.104750 restraints weight = 5298.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105315 restraints weight = 3889.912| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22427 Z= 0.184 Angle : 0.662 10.325 29725 Z= 0.333 Chirality : 0.042 0.185 3403 Planarity : 0.003 0.014 3321 Dihedral : 12.944 75.652 4100 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 5.35 % Allowed : 20.68 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.16), residues: 2624 helix: 1.67 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.66 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR a 41 PHE 0.016 0.001 PHE T 53 TRP 0.009 0.001 TRP T 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (22427) covalent geometry : angle 0.66223 / 0.33 (29725) hydrogen bonds : bond 0.04892 / 3.21 ( 1681) hydrogen bonds : angle 5.39270 / 3.76 ( 5043) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 591 time to evaluate : 0.826 Fit side-chains REVERT: B 12 ASP cc_start: 0.8687 (m-30) cc_final: 0.8367 (t0) REVERT: B 64 MET cc_start: 0.9148 (mmm) cc_final: 0.8822 (mmm) REVERT: C 23 SER cc_start: 0.8591 (t) cc_final: 0.8377 (t) REVERT: C 64 MET cc_start: 0.9114 (mmt) cc_final: 0.8645 (mmm) REVERT: D 9 LYS cc_start: 0.8951 (tttt) cc_final: 0.8647 (ttpp) REVERT: E 23 SER cc_start: 0.8988 (p) cc_final: 0.8715 (p) REVERT: G 23 SER cc_start: 0.8994 (p) cc_final: 0.8707 (p) REVERT: G 41 TYR cc_start: 0.8604 (t80) cc_final: 0.8016 (t80) REVERT: H 42 MET cc_start: 0.9109 (tmm) cc_final: 0.8849 (tmm) REVERT: I 41 TYR cc_start: 0.8724 (t80) cc_final: 0.8342 (t80) REVERT: K 41 TYR cc_start: 0.8923 (t80) cc_final: 0.8393 (t80) REVERT: K 64 MET cc_start: 0.8456 (tpp) cc_final: 0.8126 (mmt) REVERT: L 41 TYR cc_start: 0.8967 (t80) cc_final: 0.8674 (t80) REVERT: M 8 MET cc_start: 0.8958 (mtm) cc_final: 0.8527 (mtt) REVERT: N 64 MET cc_start: 0.8894 (mmm) cc_final: 0.8688 (mmm) REVERT: N 65 SER cc_start: 0.9199 (t) cc_final: 0.8827 (p) REVERT: U 64 MET cc_start: 0.8750 (mmt) cc_final: 0.8357 (mmt) REVERT: V 5 THR cc_start: 0.6674 (p) cc_final: 0.6365 (t) REVERT: X 46 ASN cc_start: 0.8782 (t0) cc_final: 0.8453 (t0) REVERT: a 8 MET cc_start: 0.7868 (tpp) cc_final: 0.7499 (tpp) REVERT: a 9 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8571 (ttmm) REVERT: b 64 MET cc_start: 0.8158 (mmp) cc_final: 0.7910 (mmp) REVERT: c 9 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8376 (ptmt) REVERT: e 40 MET cc_start: 0.7683 (tpp) cc_final: 0.7382 (tpp) REVERT: e 65 SER cc_start: 0.9050 (t) cc_final: 0.8767 (p) REVERT: f 9 LYS cc_start: 0.8724 (tppt) cc_final: 0.8493 (tppt) REVERT: f 21 LYS cc_start: 0.8001 (tttt) cc_final: 0.7382 (tptt) REVERT: f 31 LEU cc_start: 0.8899 (tp) cc_final: 0.8656 (tt) REVERT: h 9 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8688 (ttmm) REVERT: h 50 LEU cc_start: 0.9217 (mt) cc_final: 0.8930 (mt) REVERT: j 42 MET cc_start: 0.8998 (tmm) cc_final: 0.8758 (tmm) REVERT: k 64 MET cc_start: 0.8926 (mmt) cc_final: 0.8549 (mmm) REVERT: l 50 LEU cc_start: 0.9386 (mt) cc_final: 0.9099 (mt) REVERT: n 8 MET cc_start: 0.7166 (tpt) cc_final: 0.5695 (ptt) outliers start: 114 outliers final: 93 residues processed: 662 average time/residue: 0.1210 time to fit residues: 131.9406 Evaluate side-chains 653 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 558 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 12 ASP Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 30 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 23 SER Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 43 MET Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 136 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.105022 restraints weight = 29750.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108394 restraints weight = 14131.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.110489 restraints weight = 7888.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111615 restraints weight = 5047.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112442 restraints weight = 3759.565| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.6509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22427 Z= 0.130 Angle : 0.633 13.459 29725 Z= 0.311 Chirality : 0.039 0.191 3403 Planarity : 0.002 0.016 3321 Dihedral : 12.512 69.407 4100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.85 % Allowed : 22.94 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2624 helix: 1.81 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.37 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR X 41 PHE 0.014 0.001 PHE Z 19 TRP 0.006 0.001 TRP Q 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22427) covalent geometry : angle 0.63302 / 0.31 (29725) hydrogen bonds : bond 0.03881 / 2.56 ( 1681) hydrogen bonds : angle 5.27500 / 3.67 ( 5043) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 600 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9016 (mmm) cc_final: 0.8611 (mmm) REVERT: C 43 MET cc_start: 0.8282 (mmm) cc_final: 0.7960 (mmm) REVERT: C 64 MET cc_start: 0.9047 (mmt) cc_final: 0.8641 (mmm) REVERT: D 9 LYS cc_start: 0.8869 (tttt) cc_final: 0.8522 (ttpp) REVERT: E 23 SER cc_start: 0.8832 (p) cc_final: 0.8579 (p) REVERT: G 23 SER cc_start: 0.8899 (p) cc_final: 0.8575 (p) REVERT: G 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8024 (t80) REVERT: I 41 TYR cc_start: 0.8643 (t80) cc_final: 0.8230 (t80) REVERT: K 64 MET cc_start: 0.8374 (tpp) cc_final: 0.8021 (mmt) REVERT: K 69 TYR cc_start: 0.7134 (m-80) cc_final: 0.6874 (m-80) REVERT: L 41 TYR cc_start: 0.8949 (t80) cc_final: 0.8517 (t80) REVERT: M 8 MET cc_start: 0.9028 (mtm) cc_final: 0.8545 (mtt) REVERT: M 9 LYS cc_start: 0.8551 (ttpt) cc_final: 0.7948 (tptt) REVERT: M 12 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8781 (t0) REVERT: N 62 ILE cc_start: 0.8192 (mm) cc_final: 0.7862 (mm) REVERT: N 64 MET cc_start: 0.8876 (mmm) cc_final: 0.8651 (mmm) REVERT: N 65 SER cc_start: 0.9140 (t) cc_final: 0.8851 (p) REVERT: O 41 TYR cc_start: 0.9178 (t80) cc_final: 0.8883 (t80) REVERT: Q 12 ASP cc_start: 0.8250 (m-30) cc_final: 0.8035 (p0) REVERT: S 42 MET cc_start: 0.8559 (tmm) cc_final: 0.8255 (tmm) REVERT: U 64 MET cc_start: 0.8651 (mmt) cc_final: 0.8228 (mmt) REVERT: V 5 THR cc_start: 0.6721 (p) cc_final: 0.6422 (t) REVERT: W 41 TYR cc_start: 0.8872 (t80) cc_final: 0.8612 (t80) REVERT: Z 40 MET cc_start: 0.8295 (mmm) cc_final: 0.7861 (mmm) REVERT: Z 64 MET cc_start: 0.8292 (mmm) cc_final: 0.7706 (mmt) REVERT: a 8 MET cc_start: 0.7712 (tpp) cc_final: 0.7331 (tpp) REVERT: a 9 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8521 (ttmm) REVERT: b 64 MET cc_start: 0.8031 (mmp) cc_final: 0.7793 (mmp) REVERT: c 9 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8372 (ptmt) REVERT: c 64 MET cc_start: 0.8650 (mmt) cc_final: 0.8214 (mmm) REVERT: e 43 MET cc_start: 0.8215 (ttm) cc_final: 0.7744 (mtp) REVERT: e 65 SER cc_start: 0.9022 (t) cc_final: 0.8753 (p) REVERT: f 21 LYS cc_start: 0.8007 (tttt) cc_final: 0.7326 (tptt) REVERT: f 43 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7704 (mpp) REVERT: g 42 MET cc_start: 0.8378 (tmm) cc_final: 0.7142 (tpt) REVERT: h 9 LYS cc_start: 0.8844 (ttpp) cc_final: 0.8636 (ttmm) REVERT: j 12 ASP cc_start: 0.7840 (m-30) cc_final: 0.7602 (t70) REVERT: j 42 MET cc_start: 0.9122 (tmm) cc_final: 0.8241 (tmm) REVERT: k 64 MET cc_start: 0.8976 (mmt) cc_final: 0.8451 (mmm) REVERT: l 42 MET cc_start: 0.9087 (tmm) cc_final: 0.8641 (tmm) REVERT: l 50 LEU cc_start: 0.9322 (mt) cc_final: 0.8981 (mt) REVERT: n 8 MET cc_start: 0.7129 (tpt) cc_final: 0.5658 (ptt) REVERT: n 42 MET cc_start: 0.7851 (tmm) cc_final: 0.7459 (tmm) outliers start: 82 outliers final: 64 residues processed: 652 average time/residue: 0.1224 time to fit residues: 131.1291 Evaluate side-chains 638 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 570 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 30 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 148 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 230 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107624 restraints weight = 29494.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110996 restraints weight = 13856.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113130 restraints weight = 7693.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.114279 restraints weight = 4871.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115072 restraints weight = 3600.248| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22427 Z= 0.131 Angle : 0.660 12.298 29725 Z= 0.321 Chirality : 0.039 0.192 3403 Planarity : 0.003 0.021 3321 Dihedral : 12.195 59.951 4100 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.33 % Allowed : 24.02 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.16), residues: 2624 helix: 1.92 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.05 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR d 41 PHE 0.019 0.001 PHE j 53 TRP 0.007 0.001 TRP G 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (22427) covalent geometry : angle 0.66022 / 0.32 (29725) hydrogen bonds : bond 0.03738 / 2.47 ( 1681) hydrogen bonds : angle 5.22909 / 3.63 ( 5043) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 610 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.8968 (mmm) cc_final: 0.8746 (mmm) REVERT: C 40 MET cc_start: 0.8013 (mmm) cc_final: 0.7807 (mmm) REVERT: C 43 MET cc_start: 0.8254 (mmm) cc_final: 0.7833 (mmm) REVERT: C 64 MET cc_start: 0.8941 (mmt) cc_final: 0.8564 (mmm) REVERT: D 9 LYS cc_start: 0.8849 (tttt) cc_final: 0.8441 (ttpp) REVERT: E 23 SER cc_start: 0.8739 (p) cc_final: 0.8500 (p) REVERT: G 41 TYR cc_start: 0.8347 (t80) cc_final: 0.8000 (t80) REVERT: H 16 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8539 (ttpt) REVERT: I 41 TYR cc_start: 0.8601 (t80) cc_final: 0.8265 (t80) REVERT: K 41 TYR cc_start: 0.8885 (t80) cc_final: 0.8548 (t80) REVERT: K 64 MET cc_start: 0.8386 (tpp) cc_final: 0.8126 (mmt) REVERT: K 69 TYR cc_start: 0.7120 (m-80) cc_final: 0.6879 (m-80) REVERT: L 41 TYR cc_start: 0.8893 (t80) cc_final: 0.8395 (t80) REVERT: M 8 MET cc_start: 0.8939 (mtm) cc_final: 0.8510 (mtt) REVERT: M 9 LYS cc_start: 0.8522 (ttpt) cc_final: 0.7794 (tptt) REVERT: M 12 ASP cc_start: 0.9006 (m-30) cc_final: 0.8764 (t0) REVERT: N 65 SER cc_start: 0.9089 (t) cc_final: 0.8857 (p) REVERT: O 41 TYR cc_start: 0.9150 (t80) cc_final: 0.8903 (t80) REVERT: P 40 MET cc_start: 0.8514 (mmm) cc_final: 0.8136 (mmm) REVERT: Q 12 ASP cc_start: 0.8178 (m-30) cc_final: 0.7899 (p0) REVERT: S 42 MET cc_start: 0.8514 (tmm) cc_final: 0.8228 (tmm) REVERT: U 64 MET cc_start: 0.8610 (mmt) cc_final: 0.8244 (mmt) REVERT: V 5 THR cc_start: 0.6728 (p) cc_final: 0.6389 (t) REVERT: Z 40 MET cc_start: 0.8271 (mmm) cc_final: 0.7932 (mmm) REVERT: Z 41 TYR cc_start: 0.9070 (t80) cc_final: 0.8442 (t80) REVERT: Z 64 MET cc_start: 0.8245 (mmm) cc_final: 0.7712 (mmt) REVERT: a 8 MET cc_start: 0.7610 (tpp) cc_final: 0.7243 (tpp) REVERT: c 9 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8229 (ptmt) REVERT: c 64 MET cc_start: 0.8672 (mmt) cc_final: 0.8226 (mmm) REVERT: e 65 SER cc_start: 0.9014 (t) cc_final: 0.8766 (p) REVERT: f 9 LYS cc_start: 0.8724 (tppt) cc_final: 0.8270 (ttmm) REVERT: f 21 LYS cc_start: 0.8037 (tttt) cc_final: 0.7326 (tptt) REVERT: f 43 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7774 (mpp) REVERT: h 43 MET cc_start: 0.7888 (mtm) cc_final: 0.7501 (mpp) REVERT: j 12 ASP cc_start: 0.7833 (m-30) cc_final: 0.7593 (t0) REVERT: j 42 MET cc_start: 0.9042 (tmm) cc_final: 0.8807 (tmm) REVERT: j 64 MET cc_start: 0.8120 (mmt) cc_final: 0.7621 (mmp) REVERT: k 64 MET cc_start: 0.8942 (mmt) cc_final: 0.8417 (mmm) REVERT: l 42 MET cc_start: 0.8987 (tmm) cc_final: 0.8594 (tmm) REVERT: l 50 LEU cc_start: 0.9238 (mt) cc_final: 0.8959 (mt) REVERT: n 8 MET cc_start: 0.7181 (tpt) cc_final: 0.5804 (ptt) REVERT: n 42 MET cc_start: 0.7789 (tmm) cc_final: 0.7458 (tmm) outliers start: 71 outliers final: 52 residues processed: 659 average time/residue: 0.1311 time to fit residues: 141.6728 Evaluate side-chains 627 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 573 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103827 restraints weight = 30209.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107183 restraints weight = 14351.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.109235 restraints weight = 7981.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110396 restraints weight = 5134.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111163 restraints weight = 3821.103| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22427 Z= 0.150 Angle : 0.692 13.475 29725 Z= 0.337 Chirality : 0.040 0.195 3403 Planarity : 0.003 0.020 3321 Dihedral : 12.438 59.811 4100 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.95 % Allowed : 24.62 % Favored : 72.42 % 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: 2.25 (0.16), residues: 2624 helix: 1.89 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.00 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR a 41 PHE 0.023 0.001 PHE j 49 TRP 0.007 0.001 TRP R 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (22427) covalent geometry : angle 0.69209 / 0.34 (29725) hydrogen bonds : bond 0.04165 / 2.74 ( 1681) hydrogen bonds : angle 5.19385 / 3.61 ( 5043) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 579 time to evaluate : 0.738 Fit side-chains REVERT: B 64 MET cc_start: 0.9071 (mmm) cc_final: 0.8769 (mmm) REVERT: C 40 MET cc_start: 0.7988 (mmm) cc_final: 0.7768 (mmm) REVERT: C 43 MET cc_start: 0.8294 (mmm) cc_final: 0.7846 (mmm) REVERT: C 64 MET cc_start: 0.8928 (mmt) cc_final: 0.8623 (mmm) REVERT: D 9 LYS cc_start: 0.8814 (tttt) cc_final: 0.8500 (ttpp) REVERT: E 23 SER cc_start: 0.8864 (p) cc_final: 0.8587 (p) REVERT: G 23 SER cc_start: 0.8983 (p) cc_final: 0.8756 (p) REVERT: G 41 TYR cc_start: 0.8623 (t80) cc_final: 0.8150 (t80) REVERT: I 41 TYR cc_start: 0.8636 (t80) cc_final: 0.8249 (t80) REVERT: I 64 MET cc_start: 0.8850 (mmt) cc_final: 0.8546 (mmp) REVERT: K 41 TYR cc_start: 0.8928 (t80) cc_final: 0.8508 (t80) REVERT: K 64 MET cc_start: 0.8391 (tpp) cc_final: 0.8103 (mmt) REVERT: K 69 TYR cc_start: 0.7219 (m-80) cc_final: 0.6973 (m-80) REVERT: L 41 TYR cc_start: 0.8941 (t80) cc_final: 0.8419 (t80) REVERT: M 8 MET cc_start: 0.8881 (mtm) cc_final: 0.8502 (mtt) REVERT: N 62 ILE cc_start: 0.8360 (mm) cc_final: 0.8066 (mm) REVERT: N 65 SER cc_start: 0.9072 (t) cc_final: 0.8834 (p) REVERT: O 41 TYR cc_start: 0.9186 (t80) cc_final: 0.8916 (t80) REVERT: P 40 MET cc_start: 0.8542 (mmm) cc_final: 0.8205 (mmm) REVERT: P 41 TYR cc_start: 0.9095 (t80) cc_final: 0.8848 (t80) REVERT: R 8 MET cc_start: 0.7555 (mpp) cc_final: 0.7304 (mpp) REVERT: U 64 MET cc_start: 0.8754 (mmt) cc_final: 0.8392 (mmt) REVERT: V 33 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7889 (tm-30) REVERT: V 53 PHE cc_start: 0.8231 (t80) cc_final: 0.8021 (t80) REVERT: W 21 LYS cc_start: 0.8483 (tptm) cc_final: 0.8238 (tptp) REVERT: Z 40 MET cc_start: 0.8352 (mmm) cc_final: 0.8040 (mmm) REVERT: Z 41 TYR cc_start: 0.9051 (t80) cc_final: 0.8416 (t80) REVERT: Z 64 MET cc_start: 0.8432 (mmm) cc_final: 0.7642 (mmt) REVERT: a 8 MET cc_start: 0.7694 (tpp) cc_final: 0.7291 (tpp) REVERT: a 9 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8627 (ttpt) REVERT: c 9 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8272 (ptmt) REVERT: d 21 LYS cc_start: 0.7936 (tttt) cc_final: 0.7513 (tptp) REVERT: e 43 MET cc_start: 0.8288 (ttm) cc_final: 0.7630 (mtp) REVERT: e 65 SER cc_start: 0.9047 (t) cc_final: 0.8801 (p) REVERT: f 9 LYS cc_start: 0.8838 (tppt) cc_final: 0.8373 (ttmm) REVERT: j 12 ASP cc_start: 0.7834 (m-30) cc_final: 0.7629 (t70) REVERT: j 42 MET cc_start: 0.9002 (tmm) cc_final: 0.8735 (tmm) REVERT: j 64 MET cc_start: 0.8208 (mmt) cc_final: 0.7697 (mmp) REVERT: k 64 MET cc_start: 0.8936 (mmt) cc_final: 0.8499 (mmm) REVERT: l 42 MET cc_start: 0.9002 (tmm) cc_final: 0.8564 (tmm) REVERT: l 50 LEU cc_start: 0.9214 (mt) cc_final: 0.8943 (mt) REVERT: n 8 MET cc_start: 0.7199 (tpt) cc_final: 0.5952 (ptt) REVERT: n 42 MET cc_start: 0.7758 (tmm) cc_final: 0.7330 (tmm) outliers start: 63 outliers final: 55 residues processed: 621 average time/residue: 0.1265 time to fit residues: 128.4275 Evaluate side-chains 616 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 560 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 52 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 150 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.122300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106190 restraints weight = 29908.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.109590 restraints weight = 14107.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111644 restraints weight = 7837.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.112825 restraints weight = 5014.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.113435 restraints weight = 3716.338| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22427 Z= 0.141 Angle : 0.718 14.117 29725 Z= 0.346 Chirality : 0.040 0.192 3403 Planarity : 0.003 0.025 3321 Dihedral : 12.307 59.768 4100 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.44 % Allowed : 25.66 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2624 helix: 1.91 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.15 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR C 41 PHE 0.035 0.001 PHE j 49 TRP 0.008 0.001 TRP X 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (22427) covalent geometry : angle 0.71809 / 0.35 (29725) hydrogen bonds : bond 0.03901 / 2.58 ( 1681) hydrogen bonds : angle 5.17550 / 3.59 ( 5043) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 581 time to evaluate : 0.788 Fit side-chains REVERT: B 64 MET cc_start: 0.8987 (mmm) cc_final: 0.8686 (mmm) REVERT: C 40 MET cc_start: 0.7985 (mmm) cc_final: 0.7741 (mmm) REVERT: C 43 MET cc_start: 0.8265 (mmm) cc_final: 0.7901 (mmt) REVERT: C 64 MET cc_start: 0.8971 (mmt) cc_final: 0.8566 (mmm) REVERT: D 9 LYS cc_start: 0.8795 (tttt) cc_final: 0.8494 (ttpp) REVERT: E 23 SER cc_start: 0.8852 (p) cc_final: 0.8561 (p) REVERT: G 41 TYR cc_start: 0.8607 (t80) cc_final: 0.8110 (t80) REVERT: I 41 TYR cc_start: 0.8639 (t80) cc_final: 0.8269 (t80) REVERT: K 41 TYR cc_start: 0.8898 (t80) cc_final: 0.8559 (t80) REVERT: K 64 MET cc_start: 0.8449 (tpp) cc_final: 0.8243 (mmt) REVERT: K 69 TYR cc_start: 0.7188 (m-80) cc_final: 0.6960 (m-80) REVERT: L 41 TYR cc_start: 0.8897 (t80) cc_final: 0.8376 (t80) REVERT: M 8 MET cc_start: 0.8801 (mtm) cc_final: 0.8490 (mtt) REVERT: N 62 ILE cc_start: 0.8330 (mm) cc_final: 0.8062 (mm) REVERT: N 65 SER cc_start: 0.9035 (t) cc_final: 0.8810 (p) REVERT: O 41 TYR cc_start: 0.9166 (t80) cc_final: 0.8926 (t80) REVERT: P 40 MET cc_start: 0.8529 (mmm) cc_final: 0.8183 (mmm) REVERT: R 8 MET cc_start: 0.7603 (mpp) cc_final: 0.7353 (mpp) REVERT: U 64 MET cc_start: 0.8670 (mmt) cc_final: 0.8266 (mmt) REVERT: V 33 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8011 (tm-30) REVERT: W 21 LYS cc_start: 0.8498 (tptm) cc_final: 0.8167 (tptp) REVERT: Y 41 TYR cc_start: 0.8766 (t80) cc_final: 0.8565 (t80) REVERT: Z 40 MET cc_start: 0.8314 (mmm) cc_final: 0.8003 (mmm) REVERT: Z 41 TYR cc_start: 0.9084 (t80) cc_final: 0.8529 (t80) REVERT: Z 64 MET cc_start: 0.8376 (mmm) cc_final: 0.7595 (mmt) REVERT: a 8 MET cc_start: 0.7658 (tpp) cc_final: 0.7263 (tpp) REVERT: c 9 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8285 (ptmt) REVERT: c 64 MET cc_start: 0.8682 (mmt) cc_final: 0.8237 (mmm) REVERT: d 21 LYS cc_start: 0.8004 (tttt) cc_final: 0.7449 (tptp) REVERT: e 43 MET cc_start: 0.8160 (ttm) cc_final: 0.7544 (mtp) REVERT: e 65 SER cc_start: 0.9003 (t) cc_final: 0.8744 (p) REVERT: f 9 LYS cc_start: 0.8842 (tppt) cc_final: 0.8354 (ttmm) REVERT: f 43 MET cc_start: 0.7986 (mpp) cc_final: 0.7756 (mpp) REVERT: i 42 MET cc_start: 0.8547 (tmm) cc_final: 0.7270 (tpt) REVERT: j 12 ASP cc_start: 0.7752 (m-30) cc_final: 0.7510 (t70) REVERT: j 42 MET cc_start: 0.9002 (tmm) cc_final: 0.8749 (tmm) REVERT: j 64 MET cc_start: 0.8169 (mmt) cc_final: 0.7677 (mmp) REVERT: k 64 MET cc_start: 0.8936 (mmt) cc_final: 0.8417 (mmm) REVERT: l 42 MET cc_start: 0.8944 (tmm) cc_final: 0.8525 (tmm) REVERT: l 50 LEU cc_start: 0.9204 (mt) cc_final: 0.8925 (mt) REVERT: n 8 MET cc_start: 0.7152 (tpt) cc_final: 0.5804 (ptt) REVERT: n 42 MET cc_start: 0.7738 (tmm) cc_final: 0.7424 (tmm) outliers start: 52 outliers final: 51 residues processed: 623 average time/residue: 0.1275 time to fit residues: 129.9433 Evaluate side-chains 618 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 566 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Z residue 31 LEU Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 220 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.102018 restraints weight = 30464.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.105290 restraints weight = 14578.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.107276 restraints weight = 8155.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108474 restraints weight = 5282.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109092 restraints weight = 3926.805| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22427 Z= 0.171 Angle : 0.737 14.983 29725 Z= 0.359 Chirality : 0.041 0.202 3403 Planarity : 0.003 0.032 3321 Dihedral : 12.679 59.983 4100 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.00 % Allowed : 25.23 % Favored : 71.76 % 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: 2.18 (0.16), residues: 2624 helix: 1.85 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.09 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR C 41 PHE 0.051 0.001 PHE j 49 TRP 0.007 0.001 TRP T 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (22427) covalent geometry : angle 0.73697 / 0.36 (29725) hydrogen bonds : bond 0.04424 / 2.92 ( 1681) hydrogen bonds : angle 5.20449 / 3.62 ( 5043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.54 seconds wall clock time: 61 minutes 5.27 seconds (3665.27 seconds total)