Starting phenix.real_space_refine on Sun Aug 24 17:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_22460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_22460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_22460.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_22460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsv_22460/08_2025/7jsv_22460.cif" } 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-2.0-5787/lib/python3.9/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: 1.39, per 1000 atoms: 0.06 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: 1.89 Conformation dependent library (CDL) restraints added in 735.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.45 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: 3.22 Time building geometry restraints manager: 2.37 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 - 16.60: 12423 16.60 - 33.19: 697 33.19 - 49.79: 287 49.79 - 66.39: 164 66.39 - 82.98: 41 Dihedral angle restraints: 13612 sinusoidal: 6109 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 13609 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: 0.05 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: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.900 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 14.868 82.982 8856 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 aren 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 covalent geometry : bond 0.01953 (22427) covalent geometry : angle 2.09753 (29725) hydrogen bonds : bond 0.16789 ( 1681) hydrogen bonds : angle 7.48958 ( 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 : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7997 (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: 0.9006 (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: 0.8906 (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: 0.8852 (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: 0.9263 (p) cc_final: 0.8912 (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: 0.7639 (tptt) REVERT: G 23 SER cc_start: 0.9259 (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: 0.8853 (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: 0.7054 (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: 0.7633 (ttpp) REVERT: S 12 ASP cc_start: 0.7660 (m-30) cc_final: 0.7359 (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: 0.8597 (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: 0.9298 (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: 0.8567 (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: 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: 0.9179 (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: 0.8456 (mmt) cc_final: 0.8236 (mmm) REVERT: l 42 MET cc_start: 0.8858 (tmm) cc_final: 0.8317 (tmm) REVERT: m 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7404 (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: 0.1265 time to fit residues: 199.7974 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 : 0.599 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103441 restraints weight = 29934.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106856 restraints weight = 14376.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108884 restraints weight = 8031.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110253 restraints weight = 5167.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110981 restraints weight = 3723.728| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22427 Z= 0.206 Angle : 0.685 8.670 29725 Z= 0.365 Chirality : 0.043 0.183 3403 Planarity : 0.004 0.016 3321 Dihedral : 17.161 89.889 4633 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.92 % Allowed : 13.88 % Favored : 81.19 % 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 aren not related in a simple way. whole: 2.35 (0.16), residues: 2624 helix: 1.16 (0.10), residues: 2091 sheet: None (None), residues: 0 loop : 3.92 (0.33), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 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 covalent geometry : bond 0.00462 (22427) covalent geometry : angle 0.68495 (29725) hydrogen bonds : bond 0.05396 ( 1681) hydrogen bonds : angle 6.07472 ( 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 838 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 733 time to evaluate : 0.724 Fit side-chains REVERT: A 9 LYS cc_start: 0.8889 (tttt) cc_final: 0.8621 (tttm) REVERT: A 39 ILE cc_start: 0.9193 (tp) cc_final: 0.8978 (tp) REVERT: B 9 LYS cc_start: 0.9081 (tttt) cc_final: 0.8707 (ttpp) REVERT: B 64 MET cc_start: 0.9222 (mmm) cc_final: 0.8972 (mmm) REVERT: C 9 LYS cc_start: 0.8474 (tttt) cc_final: 0.8233 (ttpp) REVERT: C 23 SER cc_start: 0.8341 (t) cc_final: 0.8125 (t) REVERT: D 9 LYS cc_start: 0.8957 (tttt) cc_final: 0.8459 (ttpp) REVERT: E 23 SER cc_start: 0.8595 (p) cc_final: 0.8302 (p) REVERT: F 64 MET cc_start: 0.8390 (mmm) cc_final: 0.8045 (mmm) REVERT: G 21 LYS cc_start: 0.8269 (tttt) cc_final: 0.7676 (tptt) REVERT: G 41 TYR cc_start: 0.8552 (t80) cc_final: 0.7912 (t80) REVERT: G 64 MET cc_start: 0.8912 (mmt) cc_final: 0.8633 (mmm) REVERT: H 41 TYR cc_start: 0.8719 (t80) cc_final: 0.8172 (t80) REVERT: J 23 SER cc_start: 0.7921 (p) cc_final: 0.7572 (p) REVERT: K 9 LYS cc_start: 0.8592 (tttt) cc_final: 0.8248 (tptt) REVERT: L 65 SER cc_start: 0.9392 (t) cc_final: 0.9057 (p) REVERT: M 9 LYS cc_start: 0.8199 (tttt) cc_final: 0.7996 (tptt) REVERT: M 64 MET cc_start: 0.8155 (mmt) cc_final: 0.7825 (mmt) REVERT: N 65 SER cc_start: 0.9181 (t) cc_final: 0.8624 (p) REVERT: P 33 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8583 (tm-30) REVERT: P 41 TYR cc_start: 0.9186 (t80) cc_final: 0.8915 (t80) REVERT: P 62 ILE cc_start: 0.8826 (mm) cc_final: 0.8602 (mm) REVERT: P 65 SER cc_start: 0.8910 (t) cc_final: 0.8458 (p) REVERT: Q 40 MET cc_start: 0.9087 (mmm) cc_final: 0.8592 (mmt) REVERT: R 7 LEU cc_start: 0.8132 (mp) cc_final: 0.7911 (mp) REVERT: R 42 MET cc_start: 0.8995 (tmm) cc_final: 0.8738 (tmm) REVERT: R 64 MET cc_start: 0.8863 (mmm) cc_final: 0.8344 (mmm) REVERT: S 21 LYS cc_start: 0.8537 (tptm) cc_final: 0.8288 (tptm) REVERT: T 40 MET cc_start: 0.8940 (mmm) cc_final: 0.8729 (tpp) REVERT: U 64 MET cc_start: 0.8586 (mmt) cc_final: 0.8297 (mmm) REVERT: U 65 SER cc_start: 0.9053 (OUTLIER) cc_final: 0.8840 (p) REVERT: X 46 ASN cc_start: 0.8574 (t0) cc_final: 0.8359 (t0) REVERT: Y 64 MET cc_start: 0.8647 (mmt) cc_final: 0.8405 (mmm) REVERT: Z 41 TYR cc_start: 0.9009 (t80) cc_final: 0.8576 (t80) REVERT: c 42 MET cc_start: 0.8639 (tmm) cc_final: 0.8160 (tmm) REVERT: d 15 VAL cc_start: 0.9088 (m) cc_final: 0.8831 (p) REVERT: e 65 SER cc_start: 0.9006 (t) cc_final: 0.8577 (p) REVERT: f 9 LYS cc_start: 0.8332 (tttt) cc_final: 0.8054 (tppt) REVERT: f 41 TYR cc_start: 0.9201 (t80) cc_final: 0.8976 (t80) REVERT: h 48 LYS cc_start: 0.8403 (ptmm) cc_final: 0.7887 (ptpp) REVERT: h 49 PHE cc_start: 0.8921 (m-80) cc_final: 0.8364 (m-80) REVERT: h 50 LEU cc_start: 0.9184 (mt) cc_final: 0.8910 (mt) REVERT: i 9 LYS cc_start: 0.8605 (tttt) cc_final: 0.8357 (tptt) REVERT: i 41 TYR cc_start: 0.8647 (t80) cc_final: 0.8427 (t80) REVERT: j 12 ASP cc_start: 0.8509 (p0) cc_final: 0.8090 (m-30) REVERT: j 39 ILE cc_start: 0.9613 (tp) cc_final: 0.9235 (tp) REVERT: j 42 MET cc_start: 0.9096 (tmm) cc_final: 0.8539 (tmm) REVERT: k 64 MET cc_start: 0.8931 (mmt) cc_final: 0.8705 (mmm) REVERT: l 42 MET cc_start: 0.9217 (tmm) cc_final: 0.8803 (tmm) REVERT: l 50 LEU cc_start: 0.9303 (mt) cc_final: 0.9033 (mt) REVERT: l 56 ILE cc_start: 0.9388 (tp) cc_final: 0.9172 (tp) REVERT: m 64 MET cc_start: 0.8583 (mmt) cc_final: 0.8347 (mmp) REVERT: n 40 MET cc_start: 0.8343 (mmp) cc_final: 0.7825 (mmt) REVERT: n 65 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8184 (p) REVERT: o 9 LYS cc_start: 0.8676 (tttt) cc_final: 0.8335 (ttmt) outliers start: 105 outliers final: 61 residues processed: 787 average time/residue: 0.1202 time to fit residues: 153.8971 Evaluate side-chains 688 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 625 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 30 VAL 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 N residue 26 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 65 SER 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 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 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain a residue 57 SER 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 25 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 55 ILE 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: 10.0000 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3189 r_free = 0.3189 target = 0.111738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095894 restraints weight = 30618.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.099041 restraints weight = 14711.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.100963 restraints weight = 8250.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102163 restraints weight = 5315.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102905 restraints weight = 3910.526| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22427 Z= 0.257 Angle : 0.708 9.434 29725 Z= 0.372 Chirality : 0.045 0.209 3403 Planarity : 0.003 0.020 3321 Dihedral : 16.199 89.781 4633 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 7.13 % Allowed : 15.99 % Favored : 76.88 % 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 aren not related in a simple way. whole: 2.14 (0.16), residues: 2624 helix: 1.28 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.58 (0.31), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR T 41 PHE 0.024 0.002 PHE j 53 TRP 0.009 0.001 TRP I 28 Details of bonding type rmsd covalent geometry : bond 0.00597 (22427) covalent geometry : angle 0.70819 (29725) hydrogen bonds : bond 0.05691 ( 1681) hydrogen bonds : angle 5.81808 ( 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 803 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 651 time to evaluate : 0.819 Fit side-chains REVERT: B 9 LYS cc_start: 0.9046 (tttt) cc_final: 0.8683 (ttpp) REVERT: B 12 ASP cc_start: 0.8784 (m-30) cc_final: 0.8409 (t0) REVERT: B 64 MET cc_start: 0.9358 (mmm) cc_final: 0.9129 (mmm) REVERT: C 23 SER cc_start: 0.8820 (t) cc_final: 0.8458 (t) REVERT: D 9 LYS cc_start: 0.8936 (tttt) cc_final: 0.8489 (ttpp) REVERT: E 23 SER cc_start: 0.9110 (p) cc_final: 0.8835 (p) REVERT: G 21 LYS cc_start: 0.8432 (tttt) cc_final: 0.8041 (tptt) REVERT: G 23 SER cc_start: 0.9017 (p) cc_final: 0.8680 (p) REVERT: G 41 TYR cc_start: 0.8564 (t80) cc_final: 0.8129 (t80) REVERT: I 42 MET cc_start: 0.9130 (tmm) cc_final: 0.8791 (tmm) REVERT: J 23 SER cc_start: 0.8259 (p) cc_final: 0.7870 (p) REVERT: L 9 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8348 (tptt) REVERT: L 65 SER cc_start: 0.9279 (t) cc_final: 0.9015 (p) REVERT: N 33 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8341 (tm-30) REVERT: N 64 MET cc_start: 0.8853 (mmm) cc_final: 0.8501 (mmm) REVERT: N 65 SER cc_start: 0.9214 (t) cc_final: 0.8777 (p) REVERT: P 41 TYR cc_start: 0.9169 (t80) cc_final: 0.8854 (t80) REVERT: P 62 ILE cc_start: 0.8797 (mm) cc_final: 0.8403 (mm) REVERT: P 65 SER cc_start: 0.8959 (t) cc_final: 0.8745 (p) REVERT: Q 40 MET cc_start: 0.8844 (mmm) cc_final: 0.8468 (mmt) REVERT: R 33 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8308 (tm-30) REVERT: R 42 MET cc_start: 0.8883 (tmm) cc_final: 0.8668 (tmm) REVERT: R 64 MET cc_start: 0.8922 (mmm) cc_final: 0.8715 (mmm) REVERT: T 5 THR cc_start: 0.6546 (p) cc_final: 0.5795 (t) REVERT: W 40 MET cc_start: 0.7469 (tpp) cc_final: 0.7143 (tpp) REVERT: X 46 ASN cc_start: 0.8889 (t0) cc_final: 0.8662 (t0) REVERT: Y 64 MET cc_start: 0.8532 (mmt) cc_final: 0.8321 (mmm) REVERT: Z 64 MET cc_start: 0.8457 (mmm) cc_final: 0.7475 (mmt) REVERT: a 9 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8807 (ttmm) REVERT: c 8 MET cc_start: 0.8184 (tpp) cc_final: 0.7609 (tpp) REVERT: e 44 THR cc_start: 0.9316 (m) cc_final: 0.8949 (m) REVERT: e 65 SER cc_start: 0.9070 (t) cc_final: 0.8754 (p) REVERT: f 9 LYS cc_start: 0.8404 (tttt) cc_final: 0.7936 (tppt) REVERT: f 21 LYS cc_start: 0.8001 (tttt) cc_final: 0.7571 (tptm) REVERT: h 15 VAL cc_start: 0.9080 (m) cc_final: 0.8784 (p) REVERT: h 21 LYS cc_start: 0.8251 (tttt) cc_final: 0.7835 (tptm) REVERT: h 50 LEU cc_start: 0.9252 (mt) cc_final: 0.8993 (mt) REVERT: i 9 LYS cc_start: 0.8837 (tttt) cc_final: 0.8604 (tptt) REVERT: j 39 ILE cc_start: 0.9587 (tp) cc_final: 0.9382 (tp) REVERT: k 33 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7124 (tm-30) REVERT: k 64 MET cc_start: 0.8844 (mmt) cc_final: 0.8514 (mmm) REVERT: l 50 LEU cc_start: 0.9425 (mt) cc_final: 0.9149 (mt) REVERT: m 64 MET cc_start: 0.8750 (mmt) cc_final: 0.8395 (mmt) REVERT: n 40 MET cc_start: 0.8349 (mmp) cc_final: 0.8032 (mmt) REVERT: o 41 TYR cc_start: 0.8628 (t80) cc_final: 0.8312 (t80) outliers start: 152 outliers final: 113 residues processed: 747 average time/residue: 0.1191 time to fit residues: 145.2078 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 : 0.699 ------------------------------------------------------------------------------- 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 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE 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 7 LEU Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain L residue 10 SER 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 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 30 VAL Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 26 VAL 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 P residue 10 SER Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain P residue 60 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 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 T residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE 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 V residue 62 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 65 SER 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 Z residue 47 VAL Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL 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 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 26 VAL Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 40 MET Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 60 ILE 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 e residue 61 THR Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain f residue 14 THR 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 65 SER Chi-restraints excluded: chain h residue 44 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 12 ASP Chi-restraints excluded: chain i residue 56 ILE 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 26 VAL 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 44 THR Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE 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 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: 5.9990 chunk 76 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3262 r_free = 0.3262 target = 0.117944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.101969 restraints weight = 29867.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.105319 restraints weight = 14268.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107427 restraints weight = 7991.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108693 restraints weight = 5099.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.109280 restraints weight = 3705.137| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22427 Z= 0.141 Angle : 0.596 10.902 29725 Z= 0.304 Chirality : 0.040 0.176 3403 Planarity : 0.003 0.021 3321 Dihedral : 15.023 88.991 4633 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.50 % Allowed : 19.98 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.17), residues: 2624 helix: 1.50 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 1.90 (0.35), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR c 41 PHE 0.019 0.001 PHE X 53 TRP 0.008 0.001 TRP J 28 Details of bonding type rmsd covalent geometry : bond 0.00303 (22427) covalent geometry : angle 0.59583 (29725) hydrogen bonds : bond 0.04424 ( 1681) hydrogen bonds : angle 5.50791 ( 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 759 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 663 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8679 (m-30) cc_final: 0.8294 (t0) REVERT: B 64 MET cc_start: 0.9229 (mmm) cc_final: 0.8773 (mmm) REVERT: C 23 SER cc_start: 0.8628 (t) cc_final: 0.8326 (t) REVERT: C 64 MET cc_start: 0.9132 (mmt) cc_final: 0.8759 (mmm) REVERT: D 9 LYS cc_start: 0.8893 (tttt) cc_final: 0.8586 (ttpp) REVERT: E 23 SER cc_start: 0.8944 (p) cc_final: 0.8625 (p) REVERT: G 21 LYS cc_start: 0.8402 (tttt) cc_final: 0.7876 (tptt) REVERT: G 23 SER cc_start: 0.8780 (p) cc_final: 0.8417 (p) REVERT: G 41 TYR cc_start: 0.8561 (t80) cc_final: 0.8045 (t80) REVERT: H 41 TYR cc_start: 0.8859 (t80) cc_final: 0.8531 (t80) REVERT: H 42 MET cc_start: 0.9195 (tmm) cc_final: 0.8831 (tmm) REVERT: J 23 SER cc_start: 0.7839 (p) cc_final: 0.7586 (p) REVERT: L 41 TYR cc_start: 0.8870 (t80) cc_final: 0.8294 (t80) REVERT: M 12 ASP cc_start: 0.8977 (m-30) cc_final: 0.8759 (t0) REVERT: N 41 TYR cc_start: 0.8896 (t80) cc_final: 0.8683 (t80) REVERT: N 64 MET cc_start: 0.8803 (mmm) cc_final: 0.8562 (mmm) REVERT: N 65 SER cc_start: 0.9095 (t) cc_final: 0.8736 (p) REVERT: P 41 TYR cc_start: 0.9054 (t80) cc_final: 0.8672 (t80) REVERT: P 65 SER cc_start: 0.8865 (t) cc_final: 0.8652 (p) REVERT: Q 40 MET cc_start: 0.8909 (mmm) cc_final: 0.8580 (mmt) REVERT: R 42 MET cc_start: 0.8849 (tmm) cc_final: 0.8566 (tmm) REVERT: R 64 MET cc_start: 0.8958 (mmm) cc_final: 0.8573 (mmm) REVERT: S 40 MET cc_start: 0.8499 (mmt) cc_final: 0.8234 (mmt) REVERT: T 42 MET cc_start: 0.8482 (ttp) cc_final: 0.8085 (tmm) REVERT: U 41 TYR cc_start: 0.8684 (t80) cc_final: 0.8471 (t80) REVERT: U 64 MET cc_start: 0.8645 (mmt) cc_final: 0.8222 (mmt) REVERT: X 14 THR cc_start: 0.8930 (p) cc_final: 0.8517 (t) REVERT: X 46 ASN cc_start: 0.8884 (t0) cc_final: 0.8483 (t0) REVERT: Y 41 TYR cc_start: 0.8930 (t80) cc_final: 0.8579 (t80) REVERT: Y 64 MET cc_start: 0.8396 (mmt) cc_final: 0.8095 (mmm) REVERT: a 8 MET cc_start: 0.7900 (tpp) cc_final: 0.7669 (tpp) REVERT: a 9 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8756 (ttmm) REVERT: d 33 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7851 (tm-30) REVERT: e 65 SER cc_start: 0.9013 (t) cc_final: 0.8739 (p) REVERT: f 21 LYS cc_start: 0.7847 (tttt) cc_final: 0.7385 (tptm) REVERT: f 43 MET cc_start: 0.7996 (mpp) cc_final: 0.7557 (mpp) REVERT: f 58 THR cc_start: 0.8890 (m) cc_final: 0.8621 (p) REVERT: g 42 MET cc_start: 0.8124 (tmm) cc_final: 0.7031 (tpt) REVERT: h 15 VAL cc_start: 0.9082 (m) cc_final: 0.8839 (p) REVERT: h 21 LYS cc_start: 0.8267 (tttt) cc_final: 0.7775 (tptm) REVERT: h 50 LEU cc_start: 0.9207 (mt) cc_final: 0.8935 (mt) REVERT: i 9 LYS cc_start: 0.8724 (tttt) cc_final: 0.8517 (tptt) REVERT: j 55 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8636 (pt) REVERT: k 64 MET cc_start: 0.9001 (mmt) cc_final: 0.8517 (mmm) REVERT: l 42 MET cc_start: 0.9177 (tmm) cc_final: 0.8717 (tmm) REVERT: l 50 LEU cc_start: 0.9374 (mt) cc_final: 0.9093 (mt) REVERT: m 64 MET cc_start: 0.8735 (mmt) cc_final: 0.8453 (mmt) REVERT: n 8 MET cc_start: 0.7337 (tpt) cc_final: 0.5709 (ptt) REVERT: n 40 MET cc_start: 0.8283 (mmp) cc_final: 0.7879 (mmt) outliers start: 96 outliers final: 77 residues processed: 719 average time/residue: 0.1150 time to fit residues: 135.8032 Evaluate side-chains 671 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 593 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D 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 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 7 LEU 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 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 48 LYS 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 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 10 SER 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 65 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE 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 X residue 30 VAL Chi-restraints excluded: chain Y residue 23 SER Chi-restraints excluded: chain Y residue 43 MET 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 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 60 ILE 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 23 SER Chi-restraints excluded: chain f residue 29 VAL 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 g residue 65 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 65 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 74 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3300 r_free = 0.3300 target = 0.120781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105010 restraints weight = 29464.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.108400 restraints weight = 13953.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.110477 restraints weight = 7751.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.111759 restraints weight = 4945.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.112404 restraints weight = 3596.381| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6161 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= 0.129 Angle : 0.600 11.284 29725 Z= 0.301 Chirality : 0.039 0.194 3403 Planarity : 0.003 0.019 3321 Dihedral : 14.589 89.312 4633 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.56 % Allowed : 22.33 % Favored : 74.11 % 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 aren not related in a simple way. whole: 2.30 (0.16), residues: 2624 helix: 1.73 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.99 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR X 41 PHE 0.020 0.001 PHE j 53 TRP 0.007 0.001 TRP Q 28 Details of bonding type rmsd covalent geometry : bond 0.00271 (22427) covalent geometry : angle 0.59964 (29725) hydrogen bonds : bond 0.03962 ( 1681) hydrogen bonds : angle 5.38115 ( 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 691 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 615 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8939 (tttm) cc_final: 0.8709 (tttp) REVERT: B 64 MET cc_start: 0.9102 (mmm) cc_final: 0.8801 (mmm) REVERT: C 64 MET cc_start: 0.9063 (mmt) cc_final: 0.8512 (mmm) REVERT: D 9 LYS cc_start: 0.8971 (tttt) cc_final: 0.8584 (ttpp) REVERT: E 23 SER cc_start: 0.8770 (p) cc_final: 0.8538 (p) REVERT: G 41 TYR cc_start: 0.8429 (t80) cc_final: 0.8081 (t80) REVERT: H 41 TYR cc_start: 0.8798 (t80) cc_final: 0.8505 (t80) REVERT: H 42 MET cc_start: 0.9095 (tmm) cc_final: 0.8819 (tmm) REVERT: K 41 TYR cc_start: 0.8861 (t80) cc_final: 0.8264 (t80) REVERT: K 64 MET cc_start: 0.8453 (tpp) cc_final: 0.8038 (mmt) REVERT: L 41 TYR cc_start: 0.8817 (t80) cc_final: 0.8401 (t80) REVERT: M 8 MET cc_start: 0.8592 (mmm) cc_final: 0.8392 (mmt) REVERT: N 41 TYR cc_start: 0.8921 (t80) cc_final: 0.8677 (t80) REVERT: N 65 SER cc_start: 0.9163 (t) cc_final: 0.8774 (p) REVERT: Q 64 MET cc_start: 0.8501 (mmt) cc_final: 0.7936 (mmt) REVERT: R 64 MET cc_start: 0.8896 (mmm) cc_final: 0.8571 (mmm) REVERT: S 40 MET cc_start: 0.8515 (mmt) cc_final: 0.8285 (mmt) REVERT: S 42 MET cc_start: 0.8614 (tmm) cc_final: 0.8194 (tmm) REVERT: T 42 MET cc_start: 0.8330 (ttp) cc_final: 0.8051 (tmm) REVERT: U 64 MET cc_start: 0.8689 (mmt) cc_final: 0.8273 (mmt) REVERT: X 40 MET cc_start: 0.8818 (mmm) cc_final: 0.8600 (mmm) REVERT: X 46 ASN cc_start: 0.8844 (t0) cc_final: 0.8367 (t0) REVERT: Y 41 TYR cc_start: 0.8794 (t80) cc_final: 0.8563 (t80) REVERT: Y 64 MET cc_start: 0.8289 (mmt) cc_final: 0.8054 (mmt) REVERT: a 8 MET cc_start: 0.7829 (tpp) cc_final: 0.7531 (tpp) REVERT: a 9 LYS cc_start: 0.9025 (ttmt) cc_final: 0.8740 (ttmm) REVERT: b 64 MET cc_start: 0.8114 (mmp) cc_final: 0.7806 (mmp) REVERT: c 64 MET cc_start: 0.8645 (mmt) cc_final: 0.8127 (mmm) REVERT: e 40 MET cc_start: 0.7514 (tpp) cc_final: 0.7284 (tpp) REVERT: e 65 SER cc_start: 0.9031 (t) cc_final: 0.8774 (p) REVERT: f 21 LYS cc_start: 0.7867 (tttt) cc_final: 0.7326 (tptm) REVERT: f 58 THR cc_start: 0.8891 (m) cc_final: 0.8630 (p) REVERT: h 9 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8540 (ttmm) REVERT: i 9 LYS cc_start: 0.8633 (tttt) cc_final: 0.8424 (tptt) REVERT: k 64 MET cc_start: 0.8981 (mmt) cc_final: 0.8508 (mmm) REVERT: l 42 MET cc_start: 0.9166 (tmm) cc_final: 0.8733 (tmm) REVERT: l 50 LEU cc_start: 0.9335 (mt) cc_final: 0.9051 (mt) REVERT: m 64 MET cc_start: 0.8703 (mmt) cc_final: 0.8470 (mmt) REVERT: n 8 MET cc_start: 0.7247 (tpt) cc_final: 0.5766 (ptt) REVERT: n 40 MET cc_start: 0.8289 (mmp) cc_final: 0.7913 (mmt) outliers start: 76 outliers final: 54 residues processed: 661 average time/residue: 0.1170 time to fit residues: 126.8446 Evaluate side-chains 625 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 571 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain F residue 7 LEU 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 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET 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 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 15 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 S residue 56 ILE Chi-restraints excluded: chain T 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 Y residue 43 MET Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain c 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 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 57 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 188 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 140 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 223 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3261 r_free = 0.3261 target = 0.117616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.101693 restraints weight = 29977.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.104943 restraints weight = 14255.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106997 restraints weight = 8011.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.108236 restraints weight = 5148.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108991 restraints weight = 3764.394| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22427 Z= 0.150 Angle : 0.631 12.370 29725 Z= 0.315 Chirality : 0.040 0.228 3403 Planarity : 0.003 0.014 3321 Dihedral : 14.552 89.903 4633 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.17 % Allowed : 21.90 % Favored : 73.92 % 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 aren not related in a simple way. whole: 2.24 (0.16), residues: 2624 helix: 1.74 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.71 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR C 41 PHE 0.028 0.001 PHE j 49 TRP 0.005 0.001 TRP T 28 Details of bonding type rmsd covalent geometry : bond 0.00339 (22427) covalent geometry : angle 0.63135 (29725) hydrogen bonds : bond 0.04352 ( 1681) hydrogen bonds : angle 5.31481 ( 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 688 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 599 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8964 (tttm) cc_final: 0.8762 (tttp) REVERT: B 64 MET cc_start: 0.9168 (mmm) cc_final: 0.8805 (mmm) REVERT: C 64 MET cc_start: 0.9085 (mmt) cc_final: 0.8601 (mmm) REVERT: D 9 LYS cc_start: 0.8934 (tttt) cc_final: 0.8505 (ttpp) REVERT: E 23 SER cc_start: 0.8887 (p) cc_final: 0.8644 (p) REVERT: G 41 TYR cc_start: 0.8552 (t80) cc_final: 0.8148 (t80) REVERT: H 42 MET cc_start: 0.9122 (tmm) cc_final: 0.8869 (tmm) REVERT: I 41 TYR cc_start: 0.8692 (t80) cc_final: 0.8429 (t80) REVERT: K 64 MET cc_start: 0.8423 (tpp) cc_final: 0.8126 (mmt) REVERT: L 41 TYR cc_start: 0.8852 (t80) cc_final: 0.7995 (t80) REVERT: N 65 SER cc_start: 0.9075 (t) cc_final: 0.8768 (p) REVERT: Q 64 MET cc_start: 0.8546 (mmt) cc_final: 0.8029 (mmt) REVERT: R 64 MET cc_start: 0.8916 (mmm) cc_final: 0.8544 (mmm) REVERT: S 40 MET cc_start: 0.8469 (mmt) cc_final: 0.8262 (mmt) REVERT: S 42 MET cc_start: 0.8565 (tmm) cc_final: 0.8096 (tmm) REVERT: U 64 MET cc_start: 0.8738 (mmt) cc_final: 0.8345 (mmt) REVERT: V 5 THR cc_start: 0.6574 (p) cc_final: 0.6291 (t) REVERT: W 40 MET cc_start: 0.7506 (tpp) cc_final: 0.7162 (tpp) REVERT: X 40 MET cc_start: 0.8851 (mmm) cc_final: 0.8635 (mmm) REVERT: Z 22 GLN cc_start: 0.7554 (pm20) cc_final: 0.7240 (tm-30) REVERT: Z 40 MET cc_start: 0.8368 (mmm) cc_final: 0.8050 (mmm) REVERT: a 8 MET cc_start: 0.7817 (tpp) cc_final: 0.7450 (tpp) REVERT: b 64 MET cc_start: 0.8103 (mmp) cc_final: 0.7861 (mmp) REVERT: e 40 MET cc_start: 0.7773 (tpp) cc_final: 0.7462 (tpp) REVERT: e 65 SER cc_start: 0.9037 (t) cc_final: 0.8765 (p) REVERT: f 21 LYS cc_start: 0.7873 (tttt) cc_final: 0.7305 (tptm) REVERT: g 42 MET cc_start: 0.8447 (tmm) cc_final: 0.7299 (tpt) REVERT: h 9 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8518 (ttmm) REVERT: k 64 MET cc_start: 0.8940 (mmt) cc_final: 0.8534 (mmm) REVERT: l 42 MET cc_start: 0.9105 (tmm) cc_final: 0.8676 (tmm) REVERT: l 50 LEU cc_start: 0.9366 (mt) cc_final: 0.9085 (mt) REVERT: m 64 MET cc_start: 0.8756 (mmt) cc_final: 0.8496 (mmt) REVERT: n 8 MET cc_start: 0.7159 (tpt) cc_final: 0.5788 (ptt) REVERT: n 40 MET cc_start: 0.8226 (mmp) cc_final: 0.7832 (mmt) REVERT: n 42 MET cc_start: 0.7919 (tmm) cc_final: 0.7417 (tmm) outliers start: 89 outliers final: 80 residues processed: 658 average time/residue: 0.1216 time to fit residues: 130.9570 Evaluate side-chains 646 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 566 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain D residue 7 LEU 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 34 VAL 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 43 MET 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 56 ILE Chi-restraints excluded: chain L residue 60 ILE 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 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 S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 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 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Y residue 23 SER Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 44 THR 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 d residue 60 ILE 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 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 44 THR Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE 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 m residue 40 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 136 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 241 optimal weight: 0.0770 chunk 155 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 219 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.121179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105133 restraints weight = 29714.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.108526 restraints weight = 14165.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.110571 restraints weight = 7872.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111840 restraints weight = 5076.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.112489 restraints weight = 3716.072| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6520 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= 0.133 Angle : 0.635 11.574 29725 Z= 0.313 Chirality : 0.039 0.229 3403 Planarity : 0.002 0.017 3321 Dihedral : 14.359 89.747 4633 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.80 % Allowed : 22.98 % 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 aren not related in a simple way. whole: 2.27 (0.16), residues: 2624 helix: 1.82 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.40 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR C 41 PHE 0.031 0.001 PHE j 49 TRP 0.005 0.001 TRP Q 28 Details of bonding type rmsd covalent geometry : bond 0.00290 (22427) covalent geometry : angle 0.63484 (29725) hydrogen bonds : bond 0.03935 ( 1681) hydrogen bonds : angle 5.23857 ( 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 680 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 599 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8933 (tttm) cc_final: 0.8727 (tttp) REVERT: B 64 MET cc_start: 0.9086 (mmm) cc_final: 0.8789 (mmm) REVERT: C 64 MET cc_start: 0.9028 (mmt) cc_final: 0.8579 (mmm) REVERT: D 9 LYS cc_start: 0.8943 (tttt) cc_final: 0.8511 (ttpp) REVERT: E 23 SER cc_start: 0.8802 (p) cc_final: 0.8559 (p) REVERT: F 64 MET cc_start: 0.8611 (mmt) cc_final: 0.8332 (mmm) REVERT: G 41 TYR cc_start: 0.8484 (t80) cc_final: 0.8153 (t80) REVERT: I 41 TYR cc_start: 0.8681 (t80) cc_final: 0.8371 (t80) REVERT: I 64 MET cc_start: 0.8774 (mmt) cc_final: 0.8414 (mmp) REVERT: K 41 TYR cc_start: 0.8903 (t80) cc_final: 0.8446 (t80) REVERT: K 64 MET cc_start: 0.8382 (tpp) cc_final: 0.8047 (mmt) REVERT: L 41 TYR cc_start: 0.8800 (t80) cc_final: 0.8109 (t80) REVERT: N 65 SER cc_start: 0.9069 (t) cc_final: 0.8814 (p) REVERT: Q 64 MET cc_start: 0.8448 (mmt) cc_final: 0.7923 (mmt) REVERT: R 64 MET cc_start: 0.8916 (mmm) cc_final: 0.8595 (mmm) REVERT: S 40 MET cc_start: 0.8515 (mmt) cc_final: 0.8279 (mmt) REVERT: S 42 MET cc_start: 0.8564 (tmm) cc_final: 0.8251 (tmm) REVERT: U 64 MET cc_start: 0.8674 (mmt) cc_final: 0.8237 (mmt) REVERT: V 5 THR cc_start: 0.6773 (p) cc_final: 0.6478 (t) REVERT: Y 9 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8712 (ttpt) REVERT: Z 40 MET cc_start: 0.8444 (mmm) cc_final: 0.8087 (mmm) REVERT: a 8 MET cc_start: 0.7659 (tpp) cc_final: 0.7229 (tpp) REVERT: b 64 MET cc_start: 0.8017 (mmp) cc_final: 0.7773 (mmp) REVERT: c 64 MET cc_start: 0.8647 (mmt) cc_final: 0.8179 (mmm) REVERT: e 65 SER cc_start: 0.9032 (t) cc_final: 0.8774 (p) REVERT: f 8 MET cc_start: 0.7476 (mmp) cc_final: 0.7273 (mmp) REVERT: f 21 LYS cc_start: 0.7831 (tttt) cc_final: 0.7220 (tptm) REVERT: f 48 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8224 (ptpt) REVERT: h 9 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8495 (ttmm) REVERT: k 64 MET cc_start: 0.8961 (mmt) cc_final: 0.8467 (mmm) REVERT: l 50 LEU cc_start: 0.9339 (mt) cc_final: 0.9015 (mt) REVERT: m 64 MET cc_start: 0.8685 (mmt) cc_final: 0.8466 (mmt) REVERT: n 8 MET cc_start: 0.7141 (tpt) cc_final: 0.5640 (ptt) REVERT: n 40 MET cc_start: 0.8133 (mmp) cc_final: 0.7739 (mmt) REVERT: n 42 MET cc_start: 0.7880 (tmm) cc_final: 0.7510 (tmm) outliers start: 81 outliers final: 70 residues processed: 650 average time/residue: 0.1174 time to fit residues: 125.4302 Evaluate side-chains 637 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 566 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 23 SER 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 43 MET 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 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE 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 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 R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 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 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z 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 44 THR 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 48 LYS 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 65 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 148 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3275 r_free = 0.3275 target = 0.118980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102942 restraints weight = 29756.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.106227 restraints weight = 14169.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108213 restraints weight = 7916.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109459 restraints weight = 5109.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.110092 restraints weight = 3766.581| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22427 Z= 0.149 Angle : 0.676 12.418 29725 Z= 0.330 Chirality : 0.040 0.201 3403 Planarity : 0.003 0.022 3321 Dihedral : 14.392 89.054 4633 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.03 % Allowed : 23.55 % 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 aren not related in a simple way. whole: 2.29 (0.16), residues: 2624 helix: 1.88 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.23 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR C 41 PHE 0.038 0.001 PHE j 49 TRP 0.005 0.001 TRP N 28 Details of bonding type rmsd covalent geometry : bond 0.00340 (22427) covalent geometry : angle 0.67625 (29725) hydrogen bonds : bond 0.04230 ( 1681) hydrogen bonds : angle 5.21002 ( 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 662 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 576 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9130 (mmm) cc_final: 0.8800 (mmm) REVERT: C 64 MET cc_start: 0.9050 (mmt) cc_final: 0.8580 (mmm) REVERT: D 9 LYS cc_start: 0.8905 (tttt) cc_final: 0.8496 (ttpp) REVERT: E 23 SER cc_start: 0.8869 (p) cc_final: 0.8638 (p) REVERT: F 64 MET cc_start: 0.8495 (mmt) cc_final: 0.8265 (mmm) REVERT: G 41 TYR cc_start: 0.8682 (t80) cc_final: 0.8251 (t80) REVERT: I 41 TYR cc_start: 0.8704 (t80) cc_final: 0.8384 (t80) REVERT: I 64 MET cc_start: 0.8835 (mmt) cc_final: 0.8526 (mmp) REVERT: K 41 TYR cc_start: 0.8868 (t80) cc_final: 0.8410 (t80) REVERT: K 64 MET cc_start: 0.8458 (tpp) cc_final: 0.8063 (mmt) REVERT: L 22 GLN cc_start: 0.7888 (mp10) cc_final: 0.7681 (mp10) REVERT: L 41 TYR cc_start: 0.8821 (t80) cc_final: 0.7867 (t80) REVERT: M 8 MET cc_start: 0.8593 (mmt) cc_final: 0.8138 (mtt) REVERT: N 65 SER cc_start: 0.9081 (t) cc_final: 0.8796 (p) REVERT: Q 64 MET cc_start: 0.8489 (mmt) cc_final: 0.7993 (mmt) REVERT: R 64 MET cc_start: 0.8906 (mmm) cc_final: 0.8559 (mmm) REVERT: S 40 MET cc_start: 0.8476 (mmt) cc_final: 0.8222 (mmt) REVERT: S 42 MET cc_start: 0.8501 (tmm) cc_final: 0.8151 (tmm) REVERT: U 64 MET cc_start: 0.8719 (mmt) cc_final: 0.8357 (mmt) REVERT: a 8 MET cc_start: 0.7705 (tpp) cc_final: 0.7329 (tpp) REVERT: e 65 SER cc_start: 0.9033 (t) cc_final: 0.8762 (p) REVERT: f 21 LYS cc_start: 0.7931 (tttt) cc_final: 0.7347 (tptt) REVERT: f 48 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7989 (ptpt) REVERT: h 9 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8420 (ttmm) REVERT: k 64 MET cc_start: 0.8943 (mmt) cc_final: 0.8467 (mmm) REVERT: l 50 LEU cc_start: 0.9274 (mt) cc_final: 0.8976 (mt) REVERT: m 64 MET cc_start: 0.8737 (mmt) cc_final: 0.8490 (mmt) REVERT: n 8 MET cc_start: 0.7247 (tpt) cc_final: 0.5927 (ptt) REVERT: n 40 MET cc_start: 0.8192 (mmp) cc_final: 0.7964 (mmt) REVERT: n 42 MET cc_start: 0.7752 (tmm) cc_final: 0.7352 (tmm) outliers start: 86 outliers final: 80 residues processed: 634 average time/residue: 0.1213 time to fit residues: 126.9103 Evaluate side-chains 639 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 558 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 23 SER 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 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 60 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 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE 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 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 R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 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 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE 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 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 30 VAL 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 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 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 48 LYS 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 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 40 MET 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 40 MET 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 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: 20.0000 chunk 157 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.118787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.102461 restraints weight = 30046.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105803 restraints weight = 14466.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107819 restraints weight = 8103.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109048 restraints weight = 5248.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109619 restraints weight = 3867.528| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22427 Z= 0.156 Angle : 0.703 14.600 29725 Z= 0.341 Chirality : 0.040 0.191 3403 Planarity : 0.003 0.020 3321 Dihedral : 14.470 88.767 4633 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.75 % Allowed : 24.06 % Favored : 72.19 % 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 aren not related in a simple way. whole: 2.30 (0.16), residues: 2624 helix: 1.90 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.15 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR C 41 PHE 0.036 0.001 PHE j 49 TRP 0.006 0.001 TRP N 28 Details of bonding type rmsd covalent geometry : bond 0.00360 (22427) covalent geometry : angle 0.70324 (29725) hydrogen bonds : bond 0.04274 ( 1681) hydrogen bonds : angle 5.19538 ( 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 645 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 565 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9138 (mmm) cc_final: 0.8791 (mmm) REVERT: C 64 MET cc_start: 0.9042 (mmt) cc_final: 0.8614 (mmm) REVERT: D 9 LYS cc_start: 0.8910 (tttt) cc_final: 0.8532 (ttpp) REVERT: E 23 SER cc_start: 0.8850 (p) cc_final: 0.8597 (p) REVERT: F 64 MET cc_start: 0.8629 (mmt) cc_final: 0.8396 (mmm) REVERT: G 41 TYR cc_start: 0.8682 (t80) cc_final: 0.8265 (t80) REVERT: I 41 TYR cc_start: 0.8697 (t80) cc_final: 0.8363 (t80) REVERT: I 64 MET cc_start: 0.8836 (mmt) cc_final: 0.8529 (mmp) REVERT: K 41 TYR cc_start: 0.8900 (t80) cc_final: 0.8425 (t80) REVERT: K 64 MET cc_start: 0.8453 (tpp) cc_final: 0.8068 (mmt) REVERT: L 41 TYR cc_start: 0.8793 (t80) cc_final: 0.7736 (t80) REVERT: N 65 SER cc_start: 0.9092 (t) cc_final: 0.8835 (p) REVERT: Q 64 MET cc_start: 0.8512 (mmt) cc_final: 0.8003 (mmt) REVERT: R 64 MET cc_start: 0.8912 (mmm) cc_final: 0.8530 (mmm) REVERT: S 40 MET cc_start: 0.8485 (mmt) cc_final: 0.8240 (mmt) REVERT: S 42 MET cc_start: 0.8525 (tmm) cc_final: 0.8223 (tmm) REVERT: U 64 MET cc_start: 0.8737 (mmt) cc_final: 0.8342 (mmt) REVERT: V 33 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7892 (tm-30) REVERT: Z 40 MET cc_start: 0.8206 (mmm) cc_final: 0.7822 (mmm) REVERT: a 8 MET cc_start: 0.7713 (tpp) cc_final: 0.7314 (tpp) REVERT: d 21 LYS cc_start: 0.7945 (tttt) cc_final: 0.7562 (tptp) REVERT: e 65 SER cc_start: 0.9045 (t) cc_final: 0.8765 (p) REVERT: f 21 LYS cc_start: 0.8054 (tttt) cc_final: 0.7398 (tptt) REVERT: f 48 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (ptpt) REVERT: k 64 MET cc_start: 0.8969 (mmt) cc_final: 0.8459 (mmm) REVERT: l 50 LEU cc_start: 0.9284 (mt) cc_final: 0.8971 (mt) REVERT: m 64 MET cc_start: 0.8728 (mmt) cc_final: 0.8480 (mmt) REVERT: n 8 MET cc_start: 0.7229 (tpt) cc_final: 0.5987 (ptt) REVERT: n 40 MET cc_start: 0.7814 (mmp) cc_final: 0.7584 (mmt) REVERT: n 42 MET cc_start: 0.7870 (tmm) cc_final: 0.7450 (tmm) outliers start: 80 outliers final: 76 residues processed: 618 average time/residue: 0.1449 time to fit residues: 146.6808 Evaluate side-chains 630 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 553 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 23 SER 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 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET 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 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE 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 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 55 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 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 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Y residue 23 SER 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 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 30 VAL 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 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 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 48 LYS 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 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 40 MET 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 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 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 150 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107030 restraints weight = 29558.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110469 restraints weight = 14160.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.112584 restraints weight = 7907.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113762 restraints weight = 5082.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114531 restraints weight = 3772.005| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6898 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= 0.137 Angle : 0.714 15.680 29725 Z= 0.342 Chirality : 0.039 0.186 3403 Planarity : 0.003 0.026 3321 Dihedral : 14.306 89.750 4633 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.86 % Allowed : 25.28 % Favored : 71.86 % 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 aren not related in a simple way. whole: 2.33 (0.16), residues: 2624 helix: 1.97 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.09 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR C 41 PHE 0.032 0.001 PHE j 49 TRP 0.007 0.001 TRP N 28 Details of bonding type rmsd covalent geometry : bond 0.00307 (22427) covalent geometry : angle 0.71396 (29725) hydrogen bonds : bond 0.03788 ( 1681) hydrogen bonds : angle 5.15358 ( 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 666 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 605 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9055 (mmm) cc_final: 0.8777 (mmm) REVERT: C 64 MET cc_start: 0.9151 (mmt) cc_final: 0.8678 (mmm) REVERT: D 9 LYS cc_start: 0.8865 (tttt) cc_final: 0.8392 (ttpp) REVERT: D 43 MET cc_start: 0.7565 (mtp) cc_final: 0.7334 (mtp) REVERT: E 23 SER cc_start: 0.8813 (p) cc_final: 0.8548 (p) REVERT: G 41 TYR cc_start: 0.8597 (t80) cc_final: 0.8241 (t80) REVERT: H 16 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8505 (ttpt) REVERT: I 41 TYR cc_start: 0.8654 (t80) cc_final: 0.8393 (t80) REVERT: K 41 TYR cc_start: 0.8879 (t80) cc_final: 0.8482 (t80) REVERT: K 64 MET cc_start: 0.8451 (tpp) cc_final: 0.8177 (mmt) REVERT: L 41 TYR cc_start: 0.8719 (t80) cc_final: 0.7890 (t80) REVERT: N 65 SER cc_start: 0.8973 (t) cc_final: 0.8762 (p) REVERT: P 40 MET cc_start: 0.8602 (mmm) cc_final: 0.8254 (mmm) REVERT: Q 6 ASP cc_start: 0.7718 (t0) cc_final: 0.7269 (t70) REVERT: Q 8 MET cc_start: 0.8463 (mpp) cc_final: 0.7987 (mpp) REVERT: Q 33 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8257 (tm-30) REVERT: Q 64 MET cc_start: 0.8453 (mmt) cc_final: 0.7855 (mmt) REVERT: R 64 MET cc_start: 0.8890 (mmm) cc_final: 0.8560 (mmm) REVERT: S 21 LYS cc_start: 0.8502 (tptm) cc_final: 0.8116 (tptp) REVERT: S 40 MET cc_start: 0.8566 (mmt) cc_final: 0.8319 (mmt) REVERT: S 42 MET cc_start: 0.8528 (tmm) cc_final: 0.8248 (tmm) REVERT: T 42 MET cc_start: 0.8295 (ttp) cc_final: 0.7991 (tmm) REVERT: U 64 MET cc_start: 0.8604 (mmt) cc_final: 0.8375 (mmt) REVERT: V 33 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7855 (tm-30) REVERT: Y 41 TYR cc_start: 0.8809 (t80) cc_final: 0.8604 (t80) REVERT: Z 40 MET cc_start: 0.8164 (mmm) cc_final: 0.7794 (mmm) REVERT: Z 41 TYR cc_start: 0.9002 (t80) cc_final: 0.8425 (t80) REVERT: a 8 MET cc_start: 0.7572 (tpp) cc_final: 0.7206 (tpp) REVERT: c 9 LYS cc_start: 0.8646 (ttmt) cc_final: 0.8410 (tppt) REVERT: c 64 MET cc_start: 0.8637 (mmt) cc_final: 0.8219 (mmm) REVERT: d 15 VAL cc_start: 0.8723 (m) cc_final: 0.8517 (p) REVERT: e 65 SER cc_start: 0.9017 (t) cc_final: 0.8763 (p) REVERT: f 48 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7867 (ptpt) REVERT: k 64 MET cc_start: 0.8959 (mmt) cc_final: 0.8408 (mmm) REVERT: l 42 MET cc_start: 0.9088 (tmm) cc_final: 0.8596 (tmm) REVERT: l 50 LEU cc_start: 0.9234 (mt) cc_final: 0.8964 (mt) REVERT: n 8 MET cc_start: 0.7152 (tpt) cc_final: 0.5981 (ptt) REVERT: n 40 MET cc_start: 0.8113 (mmp) cc_final: 0.7776 (mmt) outliers start: 61 outliers final: 47 residues processed: 646 average time/residue: 0.1257 time to fit residues: 134.1140 Evaluate side-chains 620 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 572 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain F residue 23 SER 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 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER 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 57 SER Chi-restraints excluded: chain L residue 60 ILE 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 P residue 56 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T 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 56 ILE Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain b residue 30 VAL 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 29 VAL Chi-restraints excluded: chain f residue 48 LYS 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 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 43 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 230 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107718 restraints weight = 29421.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111141 restraints weight = 14092.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.113265 restraints weight = 7873.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.114430 restraints weight = 5047.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.115223 restraints weight = 3763.196| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.7034 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= 0.137 Angle : 0.720 14.386 29725 Z= 0.346 Chirality : 0.039 0.215 3403 Planarity : 0.002 0.028 3321 Dihedral : 14.309 89.872 4633 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.58 % Allowed : 26.08 % Favored : 71.34 % 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 aren not related in a simple way. whole: 2.38 (0.16), residues: 2624 helix: 2.04 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.001 TYR c 41 PHE 0.021 0.001 PHE Y 19 TRP 0.006 0.001 TRP N 28 Details of bonding type rmsd covalent geometry : bond 0.00304 (22427) covalent geometry : angle 0.72015 (29725) hydrogen bonds : bond 0.03774 ( 1681) hydrogen bonds : angle 5.14828 ( 5043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3304.68 seconds wall clock time: 58 minutes 7.46 seconds (3487.46 seconds total)