Starting phenix.real_space_refine on Thu Mar 5 11:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsv_22460/03_2026/7jsv_22460.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 205 5.16 5 C 14801 2.51 5 N 3075 2.21 5 O 4018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 2.15, per 1000 atoms: 0.10 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.49 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: 4.10 Time building geometry restraints manager: 2.66 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: 0.07 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- 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 are not related in a simple way. whole: 1.16 (0.15), residues: 2624 helix: 0.28 (0.09), residues: 2091 sheet: None (None), residues: 0 loop : 3.70 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.011 TYR b 69 PHE 0.019 0.004 PHE b 51 TRP 0.020 0.010 TRP Z 28 Details of bonding type rmsd 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 : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7996 (mmm) cc_final: 0.7758 (tpp) REVERT: A 9 LYS cc_start: 0.8726 (tttt) cc_final: 0.8372 (tttt) REVERT: A 41 TYR cc_start: 0.8508 (t80) cc_final: 0.8181 (t80) REVERT: B 7 LEU cc_start: 0.8962 (mt) cc_final: 0.8566 (mt) REVERT: B 9 LYS cc_start: 0.9005 (tttt) cc_final: 0.8408 (ttpp) REVERT: B 23 SER cc_start: 0.8826 (p) cc_final: 0.8264 (t) REVERT: B 41 TYR cc_start: 0.8907 (t80) cc_final: 0.8545 (t80) REVERT: C 9 LYS cc_start: 0.8420 (tttt) cc_final: 0.7651 (ttpp) REVERT: D 9 LYS cc_start: 0.8851 (tttt) cc_final: 0.7998 (ttpp) REVERT: D 18 THR cc_start: 0.9005 (m) cc_final: 0.8781 (p) REVERT: D 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8516 (t80) REVERT: E 9 LYS cc_start: 0.8519 (tttt) cc_final: 0.8175 (ttpt) REVERT: E 23 SER cc_start: 0.9262 (p) cc_final: 0.8913 (t) REVERT: F 23 SER cc_start: 0.8621 (p) cc_final: 0.8326 (t) REVERT: G 21 LYS cc_start: 0.8117 (tttt) cc_final: 0.7638 (tptt) REVERT: G 23 SER cc_start: 0.9260 (p) cc_final: 0.8949 (p) REVERT: G 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8063 (t80) REVERT: G 64 MET cc_start: 0.8707 (mmt) cc_final: 0.8458 (mmm) REVERT: I 21 LYS cc_start: 0.8205 (tttt) cc_final: 0.7591 (tppt) REVERT: J 42 MET cc_start: 0.9147 (tmm) cc_final: 0.8852 (tmm) REVERT: K 9 LYS cc_start: 0.7983 (tttt) cc_final: 0.7398 (tptt) REVERT: L 9 LYS cc_start: 0.8466 (tttt) cc_final: 0.8170 (ttpt) REVERT: L 65 SER cc_start: 0.9454 (t) cc_final: 0.9059 (p) REVERT: M 9 LYS cc_start: 0.7617 (tttt) cc_final: 0.7055 (ttpt) REVERT: N 9 LYS cc_start: 0.8296 (tttt) cc_final: 0.8045 (ttmt) REVERT: O 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8523 (ttmm) REVERT: O 21 LYS cc_start: 0.7695 (tttt) cc_final: 0.7318 (tptm) REVERT: P 23 SER cc_start: 0.7849 (p) cc_final: 0.7523 (p) REVERT: P 65 SER cc_start: 0.8938 (t) cc_final: 0.8518 (p) REVERT: Q 40 MET cc_start: 0.9117 (mmm) cc_final: 0.8803 (mmt) REVERT: Q 42 MET cc_start: 0.8879 (tmm) cc_final: 0.8483 (tmm) REVERT: R 12 ASP cc_start: 0.7719 (m-30) cc_final: 0.7368 (m-30) REVERT: R 16 LYS cc_start: 0.8682 (tttt) cc_final: 0.8445 (ttpt) REVERT: S 9 LYS cc_start: 0.7838 (tttt) cc_final: 0.7634 (ttpp) REVERT: S 12 ASP cc_start: 0.7659 (m-30) cc_final: 0.7358 (m-30) REVERT: S 46 ASN cc_start: 0.8507 (t0) cc_final: 0.8225 (t0) REVERT: T 9 LYS cc_start: 0.8792 (tttt) cc_final: 0.8572 (tttt) REVERT: T 23 SER cc_start: 0.8875 (p) cc_final: 0.8596 (t) REVERT: U 8 MET cc_start: 0.7231 (mmm) cc_final: 0.6730 (tpp) REVERT: U 9 LYS cc_start: 0.7891 (tttt) cc_final: 0.7679 (ttpp) REVERT: U 41 TYR cc_start: 0.7928 (t80) cc_final: 0.7495 (t80) REVERT: V 39 ILE cc_start: 0.9518 (tp) cc_final: 0.9299 (tp) REVERT: Y 23 SER cc_start: 0.8995 (p) cc_final: 0.8708 (t) REVERT: Y 64 MET cc_start: 0.8349 (mmt) cc_final: 0.7986 (mmm) REVERT: Z 53 PHE cc_start: 0.8513 (t80) cc_final: 0.7744 (t80) REVERT: a 46 ASN cc_start: 0.8863 (t0) cc_final: 0.8568 (t0) REVERT: c 12 ASP cc_start: 0.7717 (m-30) cc_final: 0.7509 (m-30) REVERT: d 8 MET cc_start: 0.7600 (mmm) cc_final: 0.7190 (mmt) REVERT: e 8 MET cc_start: 0.7530 (mmm) cc_final: 0.7330 (mmp) REVERT: f 9 LYS cc_start: 0.8279 (tttt) cc_final: 0.8076 (tppt) REVERT: g 9 LYS cc_start: 0.8460 (tttt) cc_final: 0.8156 (ptmt) REVERT: h 50 LEU cc_start: 0.9062 (mt) cc_final: 0.8797 (mt) REVERT: i 9 LYS cc_start: 0.8399 (tttt) cc_final: 0.7801 (tptt) REVERT: i 41 TYR cc_start: 0.8488 (t80) cc_final: 0.8211 (t80) REVERT: i 65 SER cc_start: 0.9180 (t) cc_final: 0.8961 (p) REVERT: j 28 TRP cc_start: 0.8069 (m-10) cc_final: 0.7802 (m-10) REVERT: j 64 MET cc_start: 0.7877 (mmt) cc_final: 0.7584 (mmp) REVERT: k 12 ASP cc_start: 0.8234 (m-30) cc_final: 0.7966 (m-30) REVERT: k 64 MET cc_start: 0.8457 (mmt) cc_final: 0.8236 (mmm) REVERT: l 42 MET cc_start: 0.8857 (tmm) cc_final: 0.8317 (tmm) REVERT: m 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7405 (t80) REVERT: o 49 PHE cc_start: 0.8349 (m-80) cc_final: 0.8113 (m-10) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.1491 time to fit residues: 237.5652 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 : 0.903 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.119418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.103456 restraints weight = 29959.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106885 restraints weight = 14481.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109052 restraints weight = 8130.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110386 restraints weight = 5159.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111072 restraints weight = 3715.061| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4308 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= 0.210 Angle : 0.686 8.366 29725 Z= 0.367 Chirality : 0.043 0.192 3403 Planarity : 0.004 0.018 3321 Dihedral : 17.086 89.993 4633 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.69 % Allowed : 14.12 % 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 are not related in a simple way. whole: 2.40 (0.16), residues: 2624 helix: 1.21 (0.10), residues: 2091 sheet: None (None), residues: 0 loop : 3.89 (0.33), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.002 TYR R 41 PHE 0.025 0.002 PHE C 49 TRP 0.009 0.001 TRP I 28 Details of bonding type rmsd covalent geometry : bond 0.00470 (22427) covalent geometry : angle 0.68551 (29725) hydrogen bonds : bond 0.05320 ( 1681) hydrogen bonds : angle 6.01897 ( 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 837 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 737 time to evaluate : 0.822 Fit side-chains REVERT: A 9 LYS cc_start: 0.8896 (tttt) cc_final: 0.8650 (tttm) REVERT: B 9 LYS cc_start: 0.9077 (tttt) cc_final: 0.8706 (ttpp) REVERT: B 64 MET cc_start: 0.9215 (mmm) cc_final: 0.9009 (mmm) REVERT: C 9 LYS cc_start: 0.8494 (tttt) cc_final: 0.8188 (ttpp) REVERT: D 9 LYS cc_start: 0.8932 (tttt) cc_final: 0.8433 (ttpp) REVERT: E 23 SER cc_start: 0.8632 (p) cc_final: 0.8347 (p) REVERT: F 64 MET cc_start: 0.8363 (mmm) cc_final: 0.8057 (mmm) REVERT: G 21 LYS cc_start: 0.8262 (tttt) cc_final: 0.7679 (tptt) REVERT: G 41 TYR cc_start: 0.8554 (t80) cc_final: 0.8017 (t80) REVERT: G 64 MET cc_start: 0.8916 (mmt) cc_final: 0.8652 (mmm) REVERT: H 41 TYR cc_start: 0.8727 (t80) cc_final: 0.8210 (t80) REVERT: J 23 SER cc_start: 0.7901 (p) cc_final: 0.7537 (p) REVERT: K 9 LYS cc_start: 0.8580 (tttt) cc_final: 0.8209 (tptt) REVERT: K 21 LYS cc_start: 0.8364 (tttt) cc_final: 0.8155 (tptp) REVERT: L 65 SER cc_start: 0.9377 (t) cc_final: 0.9056 (p) REVERT: M 9 LYS cc_start: 0.8244 (tttt) cc_final: 0.8029 (tptt) REVERT: M 64 MET cc_start: 0.8145 (mmt) cc_final: 0.7878 (mmt) REVERT: N 65 SER cc_start: 0.9172 (t) cc_final: 0.8628 (p) REVERT: P 33 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8563 (tm-30) REVERT: P 41 TYR cc_start: 0.9188 (t80) cc_final: 0.8905 (t80) REVERT: P 65 SER cc_start: 0.8909 (t) cc_final: 0.8404 (p) REVERT: Q 40 MET cc_start: 0.9088 (mmm) cc_final: 0.8597 (mmt) REVERT: R 7 LEU cc_start: 0.8118 (mp) cc_final: 0.7903 (mp) REVERT: R 42 MET cc_start: 0.8992 (tmm) cc_final: 0.8682 (tmm) REVERT: R 64 MET cc_start: 0.8851 (mmm) cc_final: 0.8600 (mmm) REVERT: S 21 LYS cc_start: 0.8553 (tptm) cc_final: 0.8155 (tptm) REVERT: T 40 MET cc_start: 0.8944 (mmm) cc_final: 0.8739 (tpp) REVERT: U 41 TYR cc_start: 0.8622 (t80) cc_final: 0.8360 (t80) REVERT: U 64 MET cc_start: 0.8588 (mmt) cc_final: 0.8326 (mmm) REVERT: U 65 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8850 (p) REVERT: X 8 MET cc_start: 0.7912 (tpp) cc_final: 0.7442 (tpp) REVERT: X 46 ASN cc_start: 0.8571 (t0) cc_final: 0.8368 (t0) REVERT: Y 64 MET cc_start: 0.8642 (mmt) cc_final: 0.8402 (mmm) REVERT: Z 41 TYR cc_start: 0.9006 (t80) cc_final: 0.8590 (t80) REVERT: a 8 MET cc_start: 0.7731 (tpp) cc_final: 0.7499 (tpp) REVERT: c 42 MET cc_start: 0.8643 (tmm) cc_final: 0.8234 (tmm) REVERT: d 15 VAL cc_start: 0.9090 (m) cc_final: 0.8832 (p) REVERT: e 64 MET cc_start: 0.8482 (mmt) cc_final: 0.8268 (mmt) REVERT: e 65 SER cc_start: 0.9011 (t) cc_final: 0.8607 (p) REVERT: f 9 LYS cc_start: 0.8297 (tttt) cc_final: 0.8063 (tppt) REVERT: f 41 TYR cc_start: 0.9196 (t80) cc_final: 0.8978 (t80) REVERT: h 50 LEU cc_start: 0.9187 (mt) cc_final: 0.8921 (mt) REVERT: i 41 TYR cc_start: 0.8664 (t80) cc_final: 0.8448 (t80) REVERT: j 12 ASP cc_start: 0.8481 (p0) cc_final: 0.8008 (m-30) REVERT: j 39 ILE cc_start: 0.9613 (tp) cc_final: 0.9248 (tp) REVERT: j 42 MET cc_start: 0.9099 (tmm) cc_final: 0.8561 (tmm) REVERT: j 58 THR cc_start: 0.8801 (m) cc_final: 0.8577 (p) REVERT: l 42 MET cc_start: 0.9208 (tmm) cc_final: 0.8841 (tmm) REVERT: l 50 LEU cc_start: 0.9314 (mt) cc_final: 0.9056 (mt) REVERT: l 56 ILE cc_start: 0.9385 (tp) cc_final: 0.9171 (tp) REVERT: m 64 MET cc_start: 0.8587 (mmt) cc_final: 0.8385 (mmp) REVERT: n 40 MET cc_start: 0.8328 (mmp) cc_final: 0.7819 (mmt) REVERT: n 65 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8180 (p) REVERT: o 9 LYS cc_start: 0.8695 (tttt) cc_final: 0.8394 (ttmt) outliers start: 100 outliers final: 58 residues processed: 788 average time/residue: 0.1333 time to fit residues: 172.2876 Evaluate side-chains 673 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 613 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 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 29 VAL Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain V residue 34 VAL Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 61 THR Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain i residue 35 VAL Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain 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: 1.9990 chunk 90 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 198 optimal weight: 30.0000 chunk 182 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 146 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.120615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.104853 restraints weight = 29474.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108335 restraints weight = 13964.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110468 restraints weight = 7674.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111753 restraints weight = 4848.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112368 restraints weight = 3507.156| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22427 Z= 0.147 Angle : 0.595 9.805 29725 Z= 0.309 Chirality : 0.040 0.187 3403 Planarity : 0.003 0.019 3321 Dihedral : 15.023 89.070 4633 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 4.13 % Allowed : 18.39 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.16), residues: 2624 helix: 1.54 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.52 (0.31), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR P 41 PHE 0.020 0.001 PHE j 53 TRP 0.006 0.001 TRP I 28 Details of bonding type rmsd covalent geometry : bond 0.00309 (22427) covalent geometry : angle 0.59549 (29725) hydrogen bonds : bond 0.04425 ( 1681) hydrogen bonds : angle 5.65801 ( 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 737 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 649 time to evaluate : 0.781 Fit side-chains REVERT: A 9 LYS cc_start: 0.8956 (tttt) cc_final: 0.8749 (tttp) REVERT: B 9 LYS cc_start: 0.8916 (tttt) cc_final: 0.8574 (ttpp) REVERT: B 12 ASP cc_start: 0.8631 (m-30) cc_final: 0.8297 (t0) REVERT: B 64 MET cc_start: 0.9233 (mmm) cc_final: 0.8951 (mmm) REVERT: D 9 LYS cc_start: 0.8839 (tttt) cc_final: 0.8475 (ttpp) REVERT: E 21 LYS cc_start: 0.8234 (tptt) cc_final: 0.7912 (tppt) REVERT: E 23 SER cc_start: 0.8903 (p) cc_final: 0.8633 (p) REVERT: F 64 MET cc_start: 0.8498 (mmm) cc_final: 0.8286 (mmm) REVERT: G 21 LYS cc_start: 0.8270 (tttt) cc_final: 0.7712 (tptt) REVERT: G 23 SER cc_start: 0.8724 (p) cc_final: 0.8417 (p) REVERT: G 41 TYR cc_start: 0.8436 (t80) cc_final: 0.8007 (t80) REVERT: H 41 TYR cc_start: 0.8626 (t80) cc_final: 0.8352 (t80) REVERT: H 42 MET cc_start: 0.9255 (tmm) cc_final: 0.8898 (tmm) REVERT: J 8 MET cc_start: 0.7723 (tpp) cc_final: 0.7464 (tpp) REVERT: L 64 MET cc_start: 0.8734 (mmm) cc_final: 0.8248 (mmm) REVERT: N 62 ILE cc_start: 0.8815 (mm) cc_final: 0.8595 (mt) REVERT: N 64 MET cc_start: 0.8825 (mmm) cc_final: 0.8552 (mmm) REVERT: N 65 SER cc_start: 0.9091 (t) cc_final: 0.8688 (p) REVERT: P 41 TYR cc_start: 0.9135 (t80) cc_final: 0.8814 (t80) REVERT: P 62 ILE cc_start: 0.8707 (mm) cc_final: 0.8449 (tp) REVERT: P 65 SER cc_start: 0.8831 (t) cc_final: 0.8621 (p) REVERT: Q 40 MET cc_start: 0.8987 (mmm) cc_final: 0.8581 (mmt) REVERT: Q 64 MET cc_start: 0.8592 (mmt) cc_final: 0.8215 (mmt) REVERT: T 42 MET cc_start: 0.8583 (ttp) cc_final: 0.8144 (tmm) REVERT: U 41 TYR cc_start: 0.8592 (t80) cc_final: 0.8388 (t80) REVERT: X 40 MET cc_start: 0.8563 (mmm) cc_final: 0.8338 (mmm) REVERT: X 46 ASN cc_start: 0.8691 (t0) cc_final: 0.8202 (t0) REVERT: Y 41 TYR cc_start: 0.8859 (t80) cc_final: 0.8613 (t80) REVERT: Y 64 MET cc_start: 0.8568 (mmt) cc_final: 0.8282 (mmt) REVERT: Z 8 MET cc_start: 0.7402 (tpp) cc_final: 0.7089 (mmm) REVERT: Z 41 TYR cc_start: 0.9014 (t80) cc_final: 0.8514 (t80) REVERT: Z 64 MET cc_start: 0.8396 (mmm) cc_final: 0.7622 (mmt) REVERT: a 8 MET cc_start: 0.7655 (tpp) cc_final: 0.7318 (tpp) REVERT: c 64 MET cc_start: 0.8581 (mmt) cc_final: 0.7895 (mmm) REVERT: e 65 SER cc_start: 0.9072 (t) cc_final: 0.8709 (p) REVERT: f 9 LYS cc_start: 0.8265 (tttt) cc_final: 0.8055 (tppt) REVERT: g 42 MET cc_start: 0.8369 (tmm) cc_final: 0.7068 (tpt) REVERT: h 6 ASP cc_start: 0.5489 (p0) cc_final: 0.4251 (m-30) REVERT: h 9 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8402 (ttpp) REVERT: h 15 VAL cc_start: 0.8901 (m) cc_final: 0.8565 (p) REVERT: h 43 MET cc_start: 0.7533 (mtm) cc_final: 0.7333 (mpp) REVERT: h 50 LEU cc_start: 0.9151 (mt) cc_final: 0.8826 (mt) REVERT: j 39 ILE cc_start: 0.9596 (tp) cc_final: 0.9258 (tp) REVERT: j 42 MET cc_start: 0.9010 (tmm) cc_final: 0.8404 (tmm) REVERT: j 64 MET cc_start: 0.7114 (mmp) cc_final: 0.6807 (mmt) REVERT: l 50 LEU cc_start: 0.9346 (mt) cc_final: 0.9014 (mt) REVERT: m 64 MET cc_start: 0.8737 (mmt) cc_final: 0.8201 (mmt) REVERT: n 40 MET cc_start: 0.8313 (mmp) cc_final: 0.8017 (mmt) REVERT: o 9 LYS cc_start: 0.8580 (tttt) cc_final: 0.8162 (ttpp) outliers start: 88 outliers final: 58 residues processed: 696 average time/residue: 0.1363 time to fit residues: 156.3010 Evaluate side-chains 655 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 597 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M 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 56 ILE 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 12 ASP Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 243 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.3294 r_free = 0.3294 target = 0.120136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.104724 restraints weight = 29728.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108000 restraints weight = 14375.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.109973 restraints weight = 8069.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111223 restraints weight = 5208.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111835 restraints weight = 3807.113| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22427 Z= 0.141 Angle : 0.597 9.178 29725 Z= 0.303 Chirality : 0.040 0.169 3403 Planarity : 0.003 0.019 3321 Dihedral : 14.509 89.802 4633 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.64 % Allowed : 19.18 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.16), residues: 2624 helix: 1.73 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 1.56 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR X 41 PHE 0.017 0.001 PHE j 53 TRP 0.006 0.001 TRP I 28 Details of bonding type rmsd covalent geometry : bond 0.00305 (22427) covalent geometry : angle 0.59716 (29725) hydrogen bonds : bond 0.04294 ( 1681) hydrogen bonds : angle 5.49864 ( 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 729 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 630 time to evaluate : 0.823 Fit side-chains REVERT: B 64 MET cc_start: 0.9201 (mmm) cc_final: 0.8891 (mmm) REVERT: C 64 MET cc_start: 0.9144 (mmt) cc_final: 0.8797 (mmm) REVERT: D 9 LYS cc_start: 0.8880 (tttt) cc_final: 0.8614 (ttpp) REVERT: D 64 MET cc_start: 0.9086 (mmm) cc_final: 0.8837 (mmt) REVERT: E 23 SER cc_start: 0.8895 (p) cc_final: 0.8618 (p) REVERT: F 9 LYS cc_start: 0.8620 (tppt) cc_final: 0.8388 (tppt) REVERT: F 12 ASP cc_start: 0.9062 (t0) cc_final: 0.8650 (t0) REVERT: F 64 MET cc_start: 0.8538 (mmm) cc_final: 0.8308 (mmm) REVERT: G 21 LYS cc_start: 0.8268 (tttt) cc_final: 0.7925 (tptt) REVERT: G 41 TYR cc_start: 0.8466 (t80) cc_final: 0.8078 (t80) REVERT: H 41 TYR cc_start: 0.8658 (t80) cc_final: 0.8307 (t80) REVERT: H 42 MET cc_start: 0.9173 (tmm) cc_final: 0.8873 (tmm) REVERT: K 21 LYS cc_start: 0.8413 (tttt) cc_final: 0.8028 (tptp) REVERT: K 64 MET cc_start: 0.8559 (tpp) cc_final: 0.8249 (mmt) REVERT: L 41 TYR cc_start: 0.8788 (t80) cc_final: 0.8453 (t80) REVERT: L 42 MET cc_start: 0.8623 (tmm) cc_final: 0.8419 (tmm) REVERT: L 64 MET cc_start: 0.8586 (mmm) cc_final: 0.8169 (mmm) REVERT: N 8 MET cc_start: 0.7509 (tpp) cc_final: 0.7276 (tpp) REVERT: N 62 ILE cc_start: 0.8842 (mm) cc_final: 0.8580 (mt) REVERT: N 65 SER cc_start: 0.9083 (t) cc_final: 0.8748 (p) REVERT: P 41 TYR cc_start: 0.9012 (t80) cc_final: 0.8662 (t80) REVERT: Q 12 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8237 (t0) REVERT: Q 40 MET cc_start: 0.8989 (mmm) cc_final: 0.8583 (mmt) REVERT: Q 64 MET cc_start: 0.8524 (mmt) cc_final: 0.7959 (mmt) REVERT: T 42 MET cc_start: 0.8609 (ttp) cc_final: 0.8108 (tmm) REVERT: X 46 ASN cc_start: 0.8736 (t0) cc_final: 0.8264 (t0) REVERT: Y 64 MET cc_start: 0.8466 (mmt) cc_final: 0.8240 (mmt) REVERT: Z 64 MET cc_start: 0.8328 (mmm) cc_final: 0.7565 (mmt) REVERT: a 8 MET cc_start: 0.7709 (tpp) cc_final: 0.7461 (tpp) REVERT: b 64 MET cc_start: 0.8286 (mmp) cc_final: 0.8056 (mmp) REVERT: c 64 MET cc_start: 0.8579 (mmt) cc_final: 0.7998 (mmm) REVERT: e 65 SER cc_start: 0.9042 (t) cc_final: 0.8710 (p) REVERT: f 9 LYS cc_start: 0.8488 (tttt) cc_final: 0.8083 (tppt) REVERT: g 42 MET cc_start: 0.8212 (tmm) cc_final: 0.7068 (tpt) REVERT: h 15 VAL cc_start: 0.9100 (m) cc_final: 0.8772 (p) REVERT: h 21 LYS cc_start: 0.8144 (tttt) cc_final: 0.7695 (tptm) REVERT: h 50 LEU cc_start: 0.9175 (mt) cc_final: 0.8893 (mt) REVERT: j 42 MET cc_start: 0.8994 (tmm) cc_final: 0.8401 (tmm) REVERT: j 64 MET cc_start: 0.7186 (mmp) cc_final: 0.6744 (mmt) REVERT: l 42 MET cc_start: 0.9183 (tmm) cc_final: 0.8757 (tmm) REVERT: l 50 LEU cc_start: 0.9320 (mt) cc_final: 0.8984 (mt) REVERT: m 64 MET cc_start: 0.8735 (mmt) cc_final: 0.8445 (mmp) REVERT: n 8 MET cc_start: 0.7280 (tpt) cc_final: 0.5659 (ptm) REVERT: n 40 MET cc_start: 0.8345 (mmp) cc_final: 0.8025 (mmt) outliers start: 99 outliers final: 74 residues processed: 690 average time/residue: 0.1299 time to fit residues: 147.5389 Evaluate side-chains 655 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 580 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET 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 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 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 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 12 ASP 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 S residue 60 ILE Chi-restraints excluded: chain T residue 34 VAL 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 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 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 i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain l residue 55 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 56 ILE 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: 5.9990 chunk 185 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 22 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.119879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.104000 restraints weight = 29548.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107398 restraints weight = 14091.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109495 restraints weight = 7836.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.110694 restraints weight = 5004.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.111497 restraints weight = 3676.874| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22427 Z= 0.137 Angle : 0.592 9.529 29725 Z= 0.298 Chirality : 0.039 0.164 3403 Planarity : 0.002 0.018 3321 Dihedral : 14.322 89.349 4633 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.36 % Allowed : 20.87 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.16), residues: 2624 helix: 1.78 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 1.05 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR N 41 PHE 0.015 0.001 PHE j 49 TRP 0.005 0.001 TRP O 28 Details of bonding type rmsd covalent geometry : bond 0.00299 (22427) covalent geometry : angle 0.59202 (29725) hydrogen bonds : bond 0.04184 ( 1681) hydrogen bonds : angle 5.38814 ( 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 715 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 622 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9117 (mmm) cc_final: 0.8817 (mmm) REVERT: C 64 MET cc_start: 0.9125 (mmt) cc_final: 0.8545 (mmm) REVERT: D 9 LYS cc_start: 0.8950 (tttt) cc_final: 0.8593 (ttpp) REVERT: D 64 MET cc_start: 0.9075 (mmm) cc_final: 0.8786 (mmt) REVERT: E 23 SER cc_start: 0.8865 (p) cc_final: 0.8539 (p) REVERT: F 64 MET cc_start: 0.8616 (mmm) cc_final: 0.8320 (mmm) REVERT: G 41 TYR cc_start: 0.8656 (t80) cc_final: 0.8123 (t80) REVERT: H 41 TYR cc_start: 0.8685 (t80) cc_final: 0.8296 (t80) REVERT: H 42 MET cc_start: 0.9144 (tmm) cc_final: 0.8861 (tmm) REVERT: K 21 LYS cc_start: 0.8451 (tttt) cc_final: 0.8115 (tptp) REVERT: K 64 MET cc_start: 0.8543 (tpp) cc_final: 0.8259 (mmt) REVERT: L 41 TYR cc_start: 0.8825 (t80) cc_final: 0.8398 (t80) REVERT: L 42 MET cc_start: 0.8595 (tmm) cc_final: 0.8351 (tmm) REVERT: L 64 MET cc_start: 0.8684 (mmm) cc_final: 0.8303 (mmm) REVERT: N 41 TYR cc_start: 0.8795 (t80) cc_final: 0.8585 (t80) REVERT: N 62 ILE cc_start: 0.8869 (mm) cc_final: 0.8488 (mm) REVERT: N 64 MET cc_start: 0.8811 (mmm) cc_final: 0.8563 (mmm) REVERT: N 65 SER cc_start: 0.9059 (t) cc_final: 0.8720 (p) REVERT: P 41 TYR cc_start: 0.8975 (t80) cc_final: 0.8685 (t80) REVERT: P 64 MET cc_start: 0.8702 (mmm) cc_final: 0.8237 (mmt) REVERT: Q 8 MET cc_start: 0.8466 (mpp) cc_final: 0.7842 (mpp) REVERT: Q 40 MET cc_start: 0.8994 (mmm) cc_final: 0.8581 (mmt) REVERT: Q 64 MET cc_start: 0.8490 (mmt) cc_final: 0.7920 (mmt) REVERT: T 42 MET cc_start: 0.8614 (ttp) cc_final: 0.8123 (tmm) REVERT: U 41 TYR cc_start: 0.8623 (t80) cc_final: 0.8395 (t80) REVERT: U 64 MET cc_start: 0.8685 (mmt) cc_final: 0.8255 (mmt) REVERT: W 40 MET cc_start: 0.7867 (mmt) cc_final: 0.7656 (tpp) REVERT: X 46 ASN cc_start: 0.8778 (t0) cc_final: 0.8346 (t0) REVERT: Y 64 MET cc_start: 0.8460 (mmt) cc_final: 0.8225 (mmt) REVERT: a 9 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8591 (ttpt) REVERT: b 64 MET cc_start: 0.8075 (mmp) cc_final: 0.7853 (mmp) REVERT: c 64 MET cc_start: 0.8641 (mmt) cc_final: 0.8125 (mmm) REVERT: d 8 MET cc_start: 0.7814 (mmm) cc_final: 0.7563 (mmm) REVERT: d 22 GLN cc_start: 0.7876 (mp10) cc_final: 0.7650 (mp10) REVERT: e 65 SER cc_start: 0.9045 (t) cc_final: 0.8770 (p) REVERT: f 9 LYS cc_start: 0.8572 (tttt) cc_final: 0.8047 (tppt) REVERT: f 43 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7804 (mpp) REVERT: h 15 VAL cc_start: 0.9121 (m) cc_final: 0.8864 (p) REVERT: h 21 LYS cc_start: 0.8212 (tttt) cc_final: 0.7893 (tptt) REVERT: h 42 MET cc_start: 0.8797 (tmm) cc_final: 0.8513 (tmm) REVERT: h 50 LEU cc_start: 0.9210 (mt) cc_final: 0.8923 (mt) REVERT: j 42 MET cc_start: 0.9027 (tmm) cc_final: 0.8391 (tmm) REVERT: j 64 MET cc_start: 0.7173 (mmp) cc_final: 0.6757 (mmt) REVERT: l 42 MET cc_start: 0.9135 (tmm) cc_final: 0.8742 (tmm) REVERT: l 50 LEU cc_start: 0.9333 (mt) cc_final: 0.8991 (mt) REVERT: m 64 MET cc_start: 0.8740 (mmt) cc_final: 0.8416 (mmt) REVERT: n 8 MET cc_start: 0.7204 (tpt) cc_final: 0.5753 (ptt) REVERT: n 40 MET cc_start: 0.8135 (mmp) cc_final: 0.7820 (mmt) outliers start: 93 outliers final: 74 residues processed: 683 average time/residue: 0.1341 time to fit residues: 150.4361 Evaluate side-chains 656 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 580 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 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 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 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 34 VAL 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 Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 61 THR 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 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 65 SER 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 55 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 188 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 140 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 223 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 207 optimal weight: 4.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.123477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107604 restraints weight = 29403.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111159 restraints weight = 13920.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113332 restraints weight = 7707.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114558 restraints weight = 4875.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.115410 restraints weight = 3557.505| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22427 Z= 0.124 Angle : 0.591 10.174 29725 Z= 0.294 Chirality : 0.039 0.157 3403 Planarity : 0.002 0.018 3321 Dihedral : 14.190 89.749 4633 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.71 % Allowed : 21.81 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.16), residues: 2624 helix: 1.87 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.56 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.001 TYR a 41 PHE 0.015 0.001 PHE Z 19 TRP 0.007 0.001 TRP T 28 Details of bonding type rmsd covalent geometry : bond 0.00260 (22427) covalent geometry : angle 0.59084 (29725) hydrogen bonds : bond 0.03766 ( 1681) hydrogen bonds : angle 5.30833 ( 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 703 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 624 time to evaluate : 0.825 Fit side-chains REVERT: B 64 MET cc_start: 0.9038 (mmm) cc_final: 0.8769 (mmm) REVERT: C 64 MET cc_start: 0.9046 (mmt) cc_final: 0.8559 (mmm) REVERT: D 9 LYS cc_start: 0.8907 (tttt) cc_final: 0.8530 (ttpp) REVERT: D 12 ASP cc_start: 0.8933 (t0) cc_final: 0.8723 (t0) REVERT: E 23 SER cc_start: 0.8777 (p) cc_final: 0.8517 (p) REVERT: F 9 LYS cc_start: 0.8689 (tppt) cc_final: 0.8433 (tppt) REVERT: F 12 ASP cc_start: 0.9128 (t0) cc_final: 0.8877 (t0) REVERT: F 55 ILE cc_start: 0.9291 (tp) cc_final: 0.9082 (tp) REVERT: G 41 TYR cc_start: 0.8647 (t80) cc_final: 0.8107 (t80) REVERT: H 19 PHE cc_start: 0.9049 (m-80) cc_final: 0.8654 (m-10) REVERT: H 41 TYR cc_start: 0.8712 (t80) cc_final: 0.8410 (t80) REVERT: I 41 TYR cc_start: 0.8666 (t80) cc_final: 0.8320 (t80) REVERT: K 21 LYS cc_start: 0.8387 (tttt) cc_final: 0.8098 (tptp) REVERT: K 41 TYR cc_start: 0.8857 (t80) cc_final: 0.8348 (t80) REVERT: K 64 MET cc_start: 0.8470 (tpp) cc_final: 0.8104 (mmt) REVERT: L 41 TYR cc_start: 0.8794 (t80) cc_final: 0.8376 (t80) REVERT: L 42 MET cc_start: 0.8592 (tmm) cc_final: 0.8267 (tmm) REVERT: L 64 MET cc_start: 0.8591 (mmm) cc_final: 0.8198 (mmm) REVERT: M 8 MET cc_start: 0.8776 (mtm) cc_final: 0.8324 (mtt) REVERT: N 64 MET cc_start: 0.8770 (mmm) cc_final: 0.8474 (mmm) REVERT: N 65 SER cc_start: 0.9131 (t) cc_final: 0.8827 (p) REVERT: Q 8 MET cc_start: 0.8449 (mpp) cc_final: 0.7856 (mpp) REVERT: Q 64 MET cc_start: 0.8432 (mmt) cc_final: 0.7866 (mmt) REVERT: T 42 MET cc_start: 0.8567 (ttp) cc_final: 0.8228 (tmm) REVERT: U 64 MET cc_start: 0.8629 (mmt) cc_final: 0.8416 (mmt) REVERT: W 40 MET cc_start: 0.7859 (mmt) cc_final: 0.7626 (tpp) REVERT: W 41 TYR cc_start: 0.8813 (t80) cc_final: 0.8449 (t80) REVERT: X 46 ASN cc_start: 0.8732 (t0) cc_final: 0.8240 (t0) REVERT: Y 64 MET cc_start: 0.8476 (mmt) cc_final: 0.8114 (mmt) REVERT: Z 40 MET cc_start: 0.8325 (mmm) cc_final: 0.7922 (mmm) REVERT: Z 64 MET cc_start: 0.8334 (mmm) cc_final: 0.7685 (mmt) REVERT: b 64 MET cc_start: 0.8032 (mmp) cc_final: 0.7772 (mmp) REVERT: c 64 MET cc_start: 0.8741 (mmt) cc_final: 0.8225 (mmm) REVERT: d 22 GLN cc_start: 0.7816 (mp10) cc_final: 0.7595 (mp10) REVERT: e 43 MET cc_start: 0.8123 (ttm) cc_final: 0.7648 (mtp) REVERT: e 65 SER cc_start: 0.9017 (t) cc_final: 0.8745 (p) REVERT: f 9 LYS cc_start: 0.8581 (tttt) cc_final: 0.8029 (tppt) REVERT: f 43 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7741 (mpp) REVERT: g 42 MET cc_start: 0.8429 (tmm) cc_final: 0.7177 (tpt) REVERT: h 42 MET cc_start: 0.8768 (tmm) cc_final: 0.8504 (tmm) REVERT: h 50 LEU cc_start: 0.9158 (mt) cc_final: 0.8858 (mt) REVERT: j 41 TYR cc_start: 0.8717 (t80) cc_final: 0.8487 (t80) REVERT: j 42 MET cc_start: 0.9026 (tmm) cc_final: 0.8321 (tmm) REVERT: l 50 LEU cc_start: 0.9274 (mt) cc_final: 0.8930 (mt) REVERT: m 64 MET cc_start: 0.8683 (mmt) cc_final: 0.8408 (mmp) REVERT: n 8 MET cc_start: 0.7325 (tpt) cc_final: 0.5841 (ptt) REVERT: n 40 MET cc_start: 0.8130 (mmp) cc_final: 0.7784 (mmt) REVERT: n 42 MET cc_start: 0.7799 (tmm) cc_final: 0.7353 (tmm) outliers start: 79 outliers final: 62 residues processed: 673 average time/residue: 0.1369 time to fit residues: 152.2912 Evaluate side-chains 642 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 579 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 7 LEU 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 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 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 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 65 SER 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 c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain 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 55 ILE Chi-restraints excluded: chain m residue 40 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 136 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.098420 restraints weight = 30341.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101663 restraints weight = 14609.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.103617 restraints weight = 8205.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104873 restraints weight = 5297.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105471 restraints weight = 3876.016| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22427 Z= 0.200 Angle : 0.683 10.911 29725 Z= 0.343 Chirality : 0.042 0.169 3403 Planarity : 0.003 0.020 3321 Dihedral : 14.789 87.268 4633 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 4.27 % Allowed : 22.84 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 2624 helix: 1.71 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.51 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.002 TYR a 41 PHE 0.037 0.001 PHE C 53 TRP 0.009 0.001 TRP T 28 Details of bonding type rmsd covalent geometry : bond 0.00469 (22427) covalent geometry : angle 0.68278 (29725) hydrogen bonds : bond 0.04988 ( 1681) hydrogen bonds : angle 5.33382 ( 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 694 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 603 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8667 (m-30) cc_final: 0.8293 (t0) REVERT: B 64 MET cc_start: 0.9242 (mmm) cc_final: 0.8799 (mmm) REVERT: C 64 MET cc_start: 0.9150 (mmt) cc_final: 0.8640 (mmm) REVERT: D 9 LYS cc_start: 0.9020 (tttt) cc_final: 0.8501 (ttpp) REVERT: E 23 SER cc_start: 0.8993 (p) cc_final: 0.8738 (p) REVERT: G 41 TYR cc_start: 0.8807 (t80) cc_final: 0.8219 (t80) REVERT: I 41 TYR cc_start: 0.8792 (t80) cc_final: 0.8373 (t80) REVERT: K 64 MET cc_start: 0.8470 (tpp) cc_final: 0.8153 (mmt) REVERT: L 41 TYR cc_start: 0.8843 (t80) cc_final: 0.7963 (t80) REVERT: L 42 MET cc_start: 0.8499 (tmm) cc_final: 0.8294 (tmm) REVERT: L 64 MET cc_start: 0.8690 (mmm) cc_final: 0.8400 (mmm) REVERT: M 8 MET cc_start: 0.8892 (mtm) cc_final: 0.8261 (mtt) REVERT: N 64 MET cc_start: 0.8896 (mmm) cc_final: 0.8608 (mmm) REVERT: N 65 SER cc_start: 0.9241 (t) cc_final: 0.8794 (p) REVERT: P 22 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7836 (mm-40) REVERT: Q 8 MET cc_start: 0.8599 (mpp) cc_final: 0.8030 (mpp) REVERT: R 6 ASP cc_start: 0.6931 (p0) cc_final: 0.6694 (p0) REVERT: T 40 MET cc_start: 0.8562 (mmm) cc_final: 0.7931 (tpp) REVERT: U 64 MET cc_start: 0.8712 (mmt) cc_final: 0.8334 (mmt) REVERT: V 5 THR cc_start: 0.6643 (p) cc_final: 0.6354 (t) REVERT: X 14 THR cc_start: 0.8958 (p) cc_final: 0.8698 (t) REVERT: X 46 ASN cc_start: 0.8787 (t0) cc_final: 0.8445 (t0) REVERT: Y 64 MET cc_start: 0.8288 (mmt) cc_final: 0.8018 (mmm) REVERT: Z 9 LYS cc_start: 0.8397 (tttt) cc_final: 0.8160 (tppt) REVERT: Z 22 GLN cc_start: 0.7650 (pm20) cc_final: 0.7112 (tm-30) REVERT: a 8 MET cc_start: 0.7933 (tpp) cc_final: 0.7598 (tpp) REVERT: b 64 MET cc_start: 0.8061 (mmp) cc_final: 0.7836 (mmp) REVERT: e 43 MET cc_start: 0.8247 (ttm) cc_final: 0.7810 (mtp) REVERT: e 65 SER cc_start: 0.9084 (t) cc_final: 0.8777 (p) REVERT: f 9 LYS cc_start: 0.8716 (tttt) cc_final: 0.8014 (tppt) REVERT: f 21 LYS cc_start: 0.7972 (tttt) cc_final: 0.7365 (tptt) REVERT: f 31 LEU cc_start: 0.8909 (tp) cc_final: 0.8646 (tt) REVERT: f 43 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7823 (mpp) REVERT: h 42 MET cc_start: 0.8864 (tmm) cc_final: 0.8487 (tmm) REVERT: h 50 LEU cc_start: 0.9271 (mt) cc_final: 0.9005 (mt) REVERT: j 42 MET cc_start: 0.9000 (tmm) cc_final: 0.8694 (tmm) REVERT: j 64 MET cc_start: 0.7214 (mmp) cc_final: 0.6822 (mmt) REVERT: l 50 LEU cc_start: 0.9300 (mt) cc_final: 0.8978 (mt) REVERT: m 64 MET cc_start: 0.8752 (mmt) cc_final: 0.8458 (mmt) REVERT: n 8 MET cc_start: 0.7165 (tpt) cc_final: 0.5703 (ptt) REVERT: n 40 MET cc_start: 0.8155 (mmp) cc_final: 0.7785 (mmt) REVERT: n 42 MET cc_start: 0.7765 (tmm) cc_final: 0.7421 (tmm) outliers start: 91 outliers final: 76 residues processed: 663 average time/residue: 0.1419 time to fit residues: 154.3313 Evaluate side-chains 654 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 577 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 C residue 34 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 6 ASP 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 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 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 10 SER Chi-restraints excluded: chain P residue 15 VAL 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 R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 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 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 65 SER 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 57 SER 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 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: 3.9990 chunk 100 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.118910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.102727 restraints weight = 29974.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106089 restraints weight = 14339.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.108157 restraints weight = 8002.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.109441 restraints weight = 5113.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.110060 restraints weight = 3725.937| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22427 Z= 0.147 Angle : 0.660 12.228 29725 Z= 0.326 Chirality : 0.039 0.202 3403 Planarity : 0.003 0.018 3321 Dihedral : 14.482 89.849 4633 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.47 % Allowed : 23.50 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2624 helix: 1.79 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.25 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR a 41 PHE 0.033 0.001 PHE C 53 TRP 0.006 0.001 TRP T 28 Details of bonding type rmsd covalent geometry : bond 0.00333 (22427) covalent geometry : angle 0.66024 (29725) hydrogen bonds : bond 0.04146 ( 1681) hydrogen bonds : angle 5.24026 ( 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 663 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 589 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9136 (mmm) cc_final: 0.8776 (mmm) REVERT: C 64 MET cc_start: 0.9052 (mmt) cc_final: 0.8564 (mmm) REVERT: D 9 LYS cc_start: 0.8934 (tttt) cc_final: 0.8466 (ttpp) REVERT: D 43 MET cc_start: 0.7843 (mtp) cc_final: 0.7504 (mtp) REVERT: E 23 SER cc_start: 0.8868 (p) cc_final: 0.8601 (p) REVERT: G 41 TYR cc_start: 0.8751 (t80) cc_final: 0.8242 (t80) REVERT: H 19 PHE cc_start: 0.8914 (m-80) cc_final: 0.8544 (m-10) REVERT: I 41 TYR cc_start: 0.8729 (t80) cc_final: 0.8388 (t80) REVERT: K 41 TYR cc_start: 0.8900 (t80) cc_final: 0.8365 (t80) REVERT: K 64 MET cc_start: 0.8417 (tpp) cc_final: 0.8063 (mmt) REVERT: L 41 TYR cc_start: 0.8802 (t80) cc_final: 0.7866 (t80) REVERT: L 42 MET cc_start: 0.8517 (tmm) cc_final: 0.8212 (tmm) REVERT: L 64 MET cc_start: 0.8700 (mmm) cc_final: 0.8312 (mmm) REVERT: M 8 MET cc_start: 0.8878 (mtm) cc_final: 0.8229 (mtt) REVERT: N 64 MET cc_start: 0.8833 (mmm) cc_final: 0.8574 (mmm) REVERT: N 65 SER cc_start: 0.9149 (t) cc_final: 0.8784 (p) REVERT: O 41 TYR cc_start: 0.9157 (t80) cc_final: 0.8935 (t80) REVERT: P 64 MET cc_start: 0.8653 (mmm) cc_final: 0.8311 (mmt) REVERT: Q 8 MET cc_start: 0.8556 (mpp) cc_final: 0.8093 (mpp) REVERT: Q 64 MET cc_start: 0.8497 (mmt) cc_final: 0.7864 (mmt) REVERT: U 64 MET cc_start: 0.8713 (mmt) cc_final: 0.8266 (mmt) REVERT: V 5 THR cc_start: 0.6726 (p) cc_final: 0.6436 (t) REVERT: W 41 TYR cc_start: 0.8895 (t80) cc_final: 0.8584 (t80) REVERT: X 14 THR cc_start: 0.8952 (p) cc_final: 0.8740 (t) REVERT: Y 64 MET cc_start: 0.8332 (mmt) cc_final: 0.8132 (mmt) REVERT: Z 9 LYS cc_start: 0.8417 (tttt) cc_final: 0.8147 (tppt) REVERT: a 8 MET cc_start: 0.7825 (tpp) cc_final: 0.7478 (tpp) REVERT: b 64 MET cc_start: 0.8012 (mmp) cc_final: 0.7783 (mmp) REVERT: c 64 MET cc_start: 0.8705 (mmt) cc_final: 0.8244 (mmm) REVERT: e 65 SER cc_start: 0.9035 (t) cc_final: 0.8739 (p) REVERT: f 9 LYS cc_start: 0.8759 (tttt) cc_final: 0.7997 (tppt) REVERT: f 21 LYS cc_start: 0.8034 (tttt) cc_final: 0.7325 (tptt) REVERT: f 43 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (mpp) REVERT: g 42 MET cc_start: 0.8380 (tmm) cc_final: 0.7191 (tpt) REVERT: h 9 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8467 (ttmm) REVERT: h 42 MET cc_start: 0.8829 (tmm) cc_final: 0.8500 (tmm) REVERT: h 50 LEU cc_start: 0.9235 (mt) cc_final: 0.8955 (mt) REVERT: j 42 MET cc_start: 0.9003 (tmm) cc_final: 0.8719 (tmm) REVERT: j 64 MET cc_start: 0.7137 (mmp) cc_final: 0.6739 (mmt) REVERT: l 42 MET cc_start: 0.9005 (tmm) cc_final: 0.8638 (tmm) REVERT: l 50 LEU cc_start: 0.9270 (mt) cc_final: 0.8977 (mt) REVERT: m 64 MET cc_start: 0.8725 (mmt) cc_final: 0.8511 (mmt) REVERT: n 8 MET cc_start: 0.7180 (tpt) cc_final: 0.5826 (ptt) REVERT: n 40 MET cc_start: 0.8190 (mmp) cc_final: 0.7809 (mmt) REVERT: n 42 MET cc_start: 0.7844 (tmm) cc_final: 0.7534 (tmm) outliers start: 74 outliers final: 64 residues processed: 641 average time/residue: 0.1379 time to fit residues: 145.9795 Evaluate side-chains 637 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 572 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 62 ILE 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 G residue 62 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain 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 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL 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 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 39 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 199 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 178 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3261 r_free = 0.3261 target = 0.117983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.101714 restraints weight = 30191.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.105068 restraints weight = 14545.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107078 restraints weight = 8185.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.108274 restraints weight = 5291.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.109093 restraints weight = 3918.579| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22427 Z= 0.158 Angle : 0.693 15.540 29725 Z= 0.340 Chirality : 0.040 0.171 3403 Planarity : 0.003 0.025 3321 Dihedral : 14.501 89.121 4633 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.61 % Allowed : 23.59 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.16), residues: 2624 helix: 1.79 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.12 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.001 TYR a 41 PHE 0.032 0.001 PHE C 53 TRP 0.006 0.001 TRP T 28 Details of bonding type rmsd covalent geometry : bond 0.00364 (22427) covalent geometry : angle 0.69303 (29725) hydrogen bonds : bond 0.04329 ( 1681) hydrogen bonds : angle 5.22164 ( 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 663 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 586 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9162 (mmm) cc_final: 0.8781 (mmm) REVERT: C 64 MET cc_start: 0.9062 (mmt) cc_final: 0.8612 (mmm) REVERT: D 9 LYS cc_start: 0.8947 (tttt) cc_final: 0.8496 (ttpp) REVERT: D 43 MET cc_start: 0.7850 (mtp) cc_final: 0.7637 (mtp) REVERT: E 15 VAL cc_start: 0.9218 (t) cc_final: 0.8879 (p) REVERT: E 23 SER cc_start: 0.8871 (p) cc_final: 0.8589 (p) REVERT: G 41 TYR cc_start: 0.8719 (t80) cc_final: 0.8274 (t80) REVERT: H 19 PHE cc_start: 0.9011 (m-80) cc_final: 0.8721 (m-10) REVERT: I 41 TYR cc_start: 0.8734 (t80) cc_final: 0.8418 (t80) REVERT: K 41 TYR cc_start: 0.8903 (t80) cc_final: 0.8360 (t80) REVERT: K 64 MET cc_start: 0.8438 (tpp) cc_final: 0.8085 (mmt) REVERT: L 41 TYR cc_start: 0.8813 (t80) cc_final: 0.7745 (t80) REVERT: L 42 MET cc_start: 0.8484 (tmm) cc_final: 0.8228 (tmm) REVERT: L 64 MET cc_start: 0.8693 (mmm) cc_final: 0.8300 (mmm) REVERT: M 8 MET cc_start: 0.8862 (mtm) cc_final: 0.8223 (mtt) REVERT: N 62 ILE cc_start: 0.8349 (mm) cc_final: 0.8031 (mm) REVERT: N 64 MET cc_start: 0.8823 (mmm) cc_final: 0.8573 (mmm) REVERT: N 65 SER cc_start: 0.9147 (t) cc_final: 0.8803 (p) REVERT: O 41 TYR cc_start: 0.9171 (t80) cc_final: 0.8954 (t80) REVERT: P 22 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7617 (mm-40) REVERT: P 64 MET cc_start: 0.8699 (mmm) cc_final: 0.8278 (mmt) REVERT: Q 8 MET cc_start: 0.8504 (mpp) cc_final: 0.8075 (mpp) REVERT: Q 64 MET cc_start: 0.8543 (mmt) cc_final: 0.7950 (mmt) REVERT: T 8 MET cc_start: 0.7666 (mpp) cc_final: 0.7376 (mpp) REVERT: U 64 MET cc_start: 0.8710 (mmt) cc_final: 0.8327 (mmt) REVERT: V 5 THR cc_start: 0.6724 (p) cc_final: 0.6419 (t) REVERT: W 21 LYS cc_start: 0.8549 (tptm) cc_final: 0.8271 (tptp) REVERT: W 41 TYR cc_start: 0.8878 (t80) cc_final: 0.8579 (t80) REVERT: Z 9 LYS cc_start: 0.8471 (tttt) cc_final: 0.8134 (tppt) REVERT: Z 33 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8151 (tm-30) REVERT: Z 40 MET cc_start: 0.8175 (mmm) cc_final: 0.7760 (mmm) REVERT: a 8 MET cc_start: 0.7819 (tpp) cc_final: 0.7465 (tpp) REVERT: b 64 MET cc_start: 0.8055 (mmp) cc_final: 0.7840 (mmp) REVERT: e 65 SER cc_start: 0.9056 (t) cc_final: 0.8771 (p) REVERT: f 9 LYS cc_start: 0.8685 (tttt) cc_final: 0.7981 (tppt) REVERT: f 21 LYS cc_start: 0.8034 (tttt) cc_final: 0.7335 (tptt) REVERT: f 43 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7741 (mpp) REVERT: h 42 MET cc_start: 0.8850 (tmm) cc_final: 0.8471 (tmm) REVERT: h 50 LEU cc_start: 0.9229 (mt) cc_final: 0.8931 (mt) REVERT: j 42 MET cc_start: 0.8924 (tmm) cc_final: 0.8650 (tmm) REVERT: j 64 MET cc_start: 0.7132 (mmp) cc_final: 0.6775 (mmt) REVERT: l 42 MET cc_start: 0.8999 (tmm) cc_final: 0.8589 (tmm) REVERT: l 50 LEU cc_start: 0.9266 (mt) cc_final: 0.8944 (mt) REVERT: m 64 MET cc_start: 0.8732 (mmt) cc_final: 0.8501 (mmt) REVERT: n 8 MET cc_start: 0.7204 (tpt) cc_final: 0.6022 (ptt) REVERT: n 42 MET cc_start: 0.7794 (tmm) cc_final: 0.7514 (tmm) outliers start: 77 outliers final: 67 residues processed: 640 average time/residue: 0.1285 time to fit residues: 135.8737 Evaluate side-chains 640 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 572 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 62 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 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 47 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 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL 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 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE 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 65 SER Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 60 ILE Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 32 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105913 restraints weight = 29707.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.109345 restraints weight = 14122.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111460 restraints weight = 7844.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.112671 restraints weight = 5020.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.113473 restraints weight = 3703.850| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22427 Z= 0.139 Angle : 0.702 16.824 29725 Z= 0.340 Chirality : 0.039 0.163 3403 Planarity : 0.003 0.029 3321 Dihedral : 14.317 89.755 4633 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.86 % Allowed : 24.39 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.16), residues: 2624 helix: 1.88 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.10 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR a 41 PHE 0.025 0.001 PHE C 53 TRP 0.007 0.001 TRP X 28 Details of bonding type rmsd covalent geometry : bond 0.00312 (22427) covalent geometry : angle 0.70157 (29725) hydrogen bonds : bond 0.03923 ( 1681) hydrogen bonds : angle 5.18732 ( 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 655 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 594 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: B 64 MET cc_start: 0.9093 (mmm) cc_final: 0.8763 (mmm) REVERT: C 43 MET cc_start: 0.8443 (mmm) cc_final: 0.8183 (mmt) REVERT: C 64 MET cc_start: 0.8969 (mmt) cc_final: 0.8575 (mmm) REVERT: D 9 LYS cc_start: 0.8937 (tttt) cc_final: 0.8488 (ttpp) REVERT: E 23 SER cc_start: 0.8846 (p) cc_final: 0.8643 (p) REVERT: G 41 TYR cc_start: 0.8641 (t80) cc_final: 0.8162 (t80) REVERT: I 41 TYR cc_start: 0.8604 (t80) cc_final: 0.8380 (t80) REVERT: I 64 MET cc_start: 0.8751 (mmt) cc_final: 0.8388 (mmp) REVERT: K 41 TYR cc_start: 0.8917 (t80) cc_final: 0.8414 (t80) REVERT: K 64 MET cc_start: 0.8442 (tpp) cc_final: 0.8175 (mmt) REVERT: L 41 TYR cc_start: 0.8767 (t80) cc_final: 0.7709 (t80) REVERT: L 42 MET cc_start: 0.8484 (tmm) cc_final: 0.8235 (tmm) REVERT: L 64 MET cc_start: 0.8586 (mmm) cc_final: 0.8238 (mmm) REVERT: M 8 MET cc_start: 0.8803 (mtm) cc_final: 0.8270 (mtt) REVERT: N 62 ILE cc_start: 0.8338 (mm) cc_final: 0.8029 (mm) REVERT: N 64 MET cc_start: 0.8828 (mmm) cc_final: 0.8618 (mmm) REVERT: N 65 SER cc_start: 0.9104 (t) cc_final: 0.8819 (p) REVERT: O 41 TYR cc_start: 0.9150 (t80) cc_final: 0.8943 (t80) REVERT: P 40 MET cc_start: 0.8618 (mmm) cc_final: 0.8118 (mmm) REVERT: P 64 MET cc_start: 0.8748 (mmm) cc_final: 0.8380 (mmt) REVERT: Q 8 MET cc_start: 0.8494 (mpp) cc_final: 0.8098 (mpp) REVERT: Q 64 MET cc_start: 0.8477 (mmt) cc_final: 0.7826 (mmt) REVERT: R 40 MET cc_start: 0.8663 (tpp) cc_final: 0.8380 (tpp) REVERT: U 64 MET cc_start: 0.8640 (mmt) cc_final: 0.8232 (mmt) REVERT: V 5 THR cc_start: 0.6690 (p) cc_final: 0.6394 (t) REVERT: V 33 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7684 (tm-30) REVERT: V 43 MET cc_start: 0.8432 (mmm) cc_final: 0.8134 (mmm) REVERT: W 21 LYS cc_start: 0.8521 (tptm) cc_final: 0.8247 (tptp) REVERT: W 41 TYR cc_start: 0.8795 (t80) cc_final: 0.8533 (t80) REVERT: Y 9 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8740 (ttpt) REVERT: Z 40 MET cc_start: 0.8166 (mmm) cc_final: 0.7762 (mmm) REVERT: Z 41 TYR cc_start: 0.9043 (t80) cc_final: 0.8513 (t80) REVERT: a 8 MET cc_start: 0.7684 (tpp) cc_final: 0.7333 (tpp) REVERT: b 64 MET cc_start: 0.8035 (mmp) cc_final: 0.7821 (mmp) REVERT: c 64 MET cc_start: 0.8759 (mmt) cc_final: 0.8310 (mmm) REVERT: d 33 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7773 (tm-30) REVERT: e 43 MET cc_start: 0.8099 (ttm) cc_final: 0.7680 (mtp) REVERT: e 65 SER cc_start: 0.9023 (t) cc_final: 0.8742 (p) REVERT: f 9 LYS cc_start: 0.8702 (tttt) cc_final: 0.8138 (tppt) REVERT: f 43 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7595 (mpp) REVERT: h 42 MET cc_start: 0.8839 (tmm) cc_final: 0.8592 (tmm) REVERT: j 42 MET cc_start: 0.8991 (tmm) cc_final: 0.8754 (tmm) REVERT: j 43 MET cc_start: 0.7600 (mtm) cc_final: 0.7360 (mtm) REVERT: l 42 MET cc_start: 0.8907 (tmm) cc_final: 0.8659 (tmm) REVERT: l 50 LEU cc_start: 0.9250 (mt) cc_final: 0.8917 (mt) REVERT: n 8 MET cc_start: 0.7184 (tpt) cc_final: 0.6020 (ptt) outliers start: 61 outliers final: 57 residues processed: 636 average time/residue: 0.1345 time to fit residues: 140.9943 Evaluate side-chains 630 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 572 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 62 ILE 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 H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 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 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 60 ILE 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 40 MET Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 56 ILE Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 43 MET Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 12 ASP Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain 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: 0.7980 chunk 237 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 230 optimal weight: 0.0040 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 236 optimal weight: 8.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.124558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.108453 restraints weight = 29391.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.111924 restraints weight = 14029.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.114046 restraints weight = 7823.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115239 restraints weight = 5004.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.116084 restraints weight = 3697.127| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22427 Z= 0.136 Angle : 0.706 13.403 29725 Z= 0.342 Chirality : 0.039 0.216 3403 Planarity : 0.003 0.027 3321 Dihedral : 14.212 89.855 4633 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.63 % Allowed : 25.33 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.16), residues: 2624 helix: 1.93 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : -0.24 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.001 TYR N 41 PHE 0.031 0.001 PHE j 49 TRP 0.008 0.001 TRP N 28 Details of bonding type rmsd covalent geometry : bond 0.00301 (22427) covalent geometry : angle 0.70625 (29725) hydrogen bonds : bond 0.03768 ( 1681) hydrogen bonds : angle 5.16533 ( 5043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.90 seconds wall clock time: 65 minutes 25.49 seconds (3925.49 seconds total)