Starting phenix.real_space_refine on Wed Jun 18 23:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsv_22460/06_2025/7jsv_22460.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z, a, c, b, e, d, g, f, i, h, k, j, m, l, o, n Time building chain proxies: 4.64, per 1000 atoms: 0.21 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: 5.98 Conformation dependent library (CDL) restraints added in 2.5 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: 2.30 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: 6.40 Time building geometry restraints manager: 6.82 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' selection = chain 'm' selection = chain 'l' selection = chain 'o' selection = chain 'n' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 38.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.130 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (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 TRP 0.020 0.010 TRP Z 28 PHE 0.019 0.004 PHE b 51 TYR 0.041 0.011 TYR b 69 Details of bonding type rmsd hydrogen bonds : bond 0.16789 ( 1681) hydrogen bonds : angle 7.48958 ( 5043) covalent geometry : bond 0.01953 (22427) covalent geometry : angle 2.09753 (29725) *********************** 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 : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.7997 (mmm) cc_final: 0.7759 (tpp) REVERT: A 9 LYS cc_start: 0.8726 (tttt) cc_final: 0.8376 (tttt) REVERT: A 41 TYR cc_start: 0.8508 (t80) cc_final: 0.8184 (t80) REVERT: B 7 LEU cc_start: 0.8962 (mt) cc_final: 0.8567 (mt) REVERT: B 9 LYS cc_start: 0.9006 (tttt) cc_final: 0.8404 (ttpp) REVERT: B 23 SER cc_start: 0.8826 (p) cc_final: 0.8337 (t) REVERT: B 41 TYR cc_start: 0.8906 (t80) cc_final: 0.8544 (t80) REVERT: C 9 LYS cc_start: 0.8420 (tttt) cc_final: 0.7650 (ttpp) REVERT: D 9 LYS cc_start: 0.8852 (tttt) cc_final: 0.8227 (ttpp) REVERT: D 18 THR cc_start: 0.9005 (m) cc_final: 0.8788 (p) REVERT: D 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8519 (t80) REVERT: E 7 LEU cc_start: 0.8976 (mt) cc_final: 0.8773 (mp) REVERT: E 9 LYS cc_start: 0.8519 (tttt) cc_final: 0.8152 (ttpt) REVERT: E 23 SER cc_start: 0.9263 (p) cc_final: 0.8908 (t) REVERT: F 23 SER cc_start: 0.8621 (p) cc_final: 0.8329 (t) REVERT: G 21 LYS cc_start: 0.8117 (tttt) cc_final: 0.7638 (tptt) REVERT: G 23 SER cc_start: 0.9259 (p) cc_final: 0.8951 (p) REVERT: G 41 TYR cc_start: 0.8469 (t80) cc_final: 0.8060 (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: 0.7592 (tppt) REVERT: J 42 MET cc_start: 0.9147 (tmm) cc_final: 0.8851 (tmm) REVERT: K 9 LYS cc_start: 0.7983 (tttt) cc_final: 0.7473 (tptt) REVERT: L 9 LYS cc_start: 0.8466 (tttt) cc_final: 0.8191 (ttpt) REVERT: L 65 SER cc_start: 0.9454 (t) cc_final: 0.9057 (p) REVERT: M 9 LYS cc_start: 0.7617 (tttt) cc_final: 0.7083 (ttpt) REVERT: N 9 LYS cc_start: 0.8296 (tttt) cc_final: 0.8049 (ttmt) REVERT: O 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8528 (ttmm) REVERT: O 21 LYS cc_start: 0.7695 (tttt) cc_final: 0.7319 (tptm) REVERT: P 23 SER cc_start: 0.7849 (p) cc_final: 0.7526 (p) REVERT: P 65 SER cc_start: 0.8938 (t) cc_final: 0.8515 (p) REVERT: Q 40 MET cc_start: 0.9117 (mmm) cc_final: 0.8802 (mmt) REVERT: Q 42 MET cc_start: 0.8879 (tmm) cc_final: 0.8485 (tmm) REVERT: R 12 ASP cc_start: 0.7719 (m-30) cc_final: 0.7366 (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: 0.7660 (m-30) cc_final: 0.7357 (m-30) REVERT: S 46 ASN cc_start: 0.8507 (t0) cc_final: 0.8289 (t0) REVERT: T 23 SER cc_start: 0.8875 (p) cc_final: 0.8591 (t) REVERT: U 8 MET cc_start: 0.7231 (mmm) cc_final: 0.6731 (tpp) REVERT: U 9 LYS cc_start: 0.7891 (tttt) cc_final: 0.7680 (ttpp) REVERT: U 41 TYR cc_start: 0.7928 (t80) cc_final: 0.7496 (t80) REVERT: V 9 LYS cc_start: 0.8531 (tttt) cc_final: 0.8290 (ttmt) REVERT: V 39 ILE cc_start: 0.9518 (tp) cc_final: 0.9312 (tp) REVERT: Y 23 SER cc_start: 0.8995 (p) cc_final: 0.8707 (t) REVERT: Y 64 MET cc_start: 0.8349 (mmt) cc_final: 0.7985 (mmm) REVERT: Z 53 PHE cc_start: 0.8513 (t80) cc_final: 0.7744 (t80) REVERT: a 46 ASN cc_start: 0.8863 (t0) cc_final: 0.8567 (t0) REVERT: c 12 ASP cc_start: 0.7717 (m-30) cc_final: 0.7508 (m-30) REVERT: d 8 MET cc_start: 0.7600 (mmm) cc_final: 0.7253 (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: 0.8075 (tppt) REVERT: g 9 LYS cc_start: 0.8460 (tttt) cc_final: 0.8158 (ptmt) REVERT: h 50 LEU cc_start: 0.9062 (mt) cc_final: 0.8796 (mt) REVERT: i 9 LYS cc_start: 0.8399 (tttt) cc_final: 0.7802 (tptt) REVERT: i 41 TYR cc_start: 0.8488 (t80) cc_final: 0.8212 (t80) REVERT: i 65 SER cc_start: 0.9179 (t) cc_final: 0.8961 (p) REVERT: j 28 TRP cc_start: 0.8069 (m-10) cc_final: 0.7805 (m-10) REVERT: j 64 MET cc_start: 0.7877 (mmt) cc_final: 0.7582 (mmp) REVERT: k 12 ASP cc_start: 0.8234 (m-30) cc_final: 0.7967 (m-30) REVERT: k 64 MET cc_start: 0.8456 (mmt) cc_final: 0.8236 (mmm) REVERT: l 42 MET cc_start: 0.8858 (tmm) cc_final: 0.8316 (tmm) REVERT: m 41 TYR cc_start: 0.7675 (t80) cc_final: 0.7404 (t80) REVERT: o 49 PHE cc_start: 0.8349 (m-80) cc_final: 0.8113 (m-10) outliers start: 0 outliers final: 0 residues processed: 999 average time/residue: 0.3144 time to fit residues: 491.4328 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 : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.125507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.109389 restraints weight = 29482.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113107 restraints weight = 14098.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115404 restraints weight = 7787.218| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22427 Z= 0.165 Angle : 0.642 8.723 29725 Z= 0.342 Chirality : 0.041 0.184 3403 Planarity : 0.003 0.018 3321 Dihedral : 16.764 89.962 4633 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.80 % Allowed : 14.35 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.16), residues: 2624 helix: 1.19 (0.10), residues: 2091 sheet: None (None), residues: 0 loop : 3.86 (0.33), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 28 PHE 0.026 0.001 PHE C 49 TYR 0.019 0.002 TYR R 41 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 1681) hydrogen bonds : angle 6.00205 ( 5043) covalent geometry : bond 0.00342 (22427) covalent geometry : angle 0.64213 (29725) *********************** 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 819 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 738 time to evaluate : 2.161 Fit side-chains REVERT: A 9 LYS cc_start: 0.8724 (tttt) cc_final: 0.8422 (tttm) REVERT: B 9 LYS cc_start: 0.9036 (tttt) cc_final: 0.8630 (ttpp) REVERT: C 9 LYS cc_start: 0.8455 (tttt) cc_final: 0.8099 (ttpp) REVERT: D 9 LYS cc_start: 0.8785 (tttt) cc_final: 0.8395 (ttpp) REVERT: G 21 LYS cc_start: 0.8254 (tttt) cc_final: 0.7530 (tptt) REVERT: G 41 TYR cc_start: 0.8424 (t80) cc_final: 0.7904 (t80) REVERT: G 51 PHE cc_start: 0.8982 (m-80) cc_final: 0.8754 (m-80) REVERT: G 64 MET cc_start: 0.8915 (mmt) cc_final: 0.8613 (mmm) REVERT: H 41 TYR cc_start: 0.8595 (t80) cc_final: 0.8090 (t80) REVERT: I 41 TYR cc_start: 0.8576 (t80) cc_final: 0.8235 (t80) REVERT: J 23 SER cc_start: 0.7700 (p) cc_final: 0.7372 (p) REVERT: K 9 LYS cc_start: 0.8335 (tttt) cc_final: 0.8009 (tptt) REVERT: K 69 TYR cc_start: 0.6837 (m-80) cc_final: 0.6483 (m-80) REVERT: L 65 SER cc_start: 0.9402 (t) cc_final: 0.9075 (p) REVERT: N 62 ILE cc_start: 0.8737 (mm) cc_final: 0.8529 (mm) REVERT: N 65 SER cc_start: 0.9101 (t) cc_final: 0.8570 (p) REVERT: P 22 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7544 (mm-40) REVERT: P 33 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8557 (tm-30) REVERT: P 41 TYR cc_start: 0.9122 (t80) cc_final: 0.8887 (t80) REVERT: P 62 ILE cc_start: 0.8821 (mm) cc_final: 0.8603 (mm) REVERT: P 65 SER cc_start: 0.8891 (t) cc_final: 0.8423 (p) REVERT: Q 41 TYR cc_start: 0.8934 (t80) cc_final: 0.8544 (t80) REVERT: R 8 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7304 (tpp) REVERT: R 64 MET cc_start: 0.8861 (mmm) cc_final: 0.8297 (mmm) REVERT: S 21 LYS cc_start: 0.8202 (tptm) cc_final: 0.7688 (tptm) REVERT: T 40 MET cc_start: 0.9042 (mmm) cc_final: 0.8837 (mmm) REVERT: U 41 TYR cc_start: 0.8480 (t80) cc_final: 0.8190 (t80) REVERT: U 64 MET cc_start: 0.8354 (mmt) cc_final: 0.7954 (mmm) REVERT: U 65 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8620 (p) REVERT: X 8 MET cc_start: 0.7968 (tpp) cc_final: 0.7424 (tpp) REVERT: Y 64 MET cc_start: 0.8559 (mmt) cc_final: 0.8269 (mmm) REVERT: Z 41 TYR cc_start: 0.9064 (t80) cc_final: 0.8679 (t80) REVERT: Z 64 MET cc_start: 0.8696 (mmt) cc_final: 0.8405 (mmm) REVERT: a 10 SER cc_start: 0.9149 (p) cc_final: 0.8885 (t) REVERT: c 42 MET cc_start: 0.8535 (tmm) cc_final: 0.8100 (tmm) REVERT: e 7 LEU cc_start: 0.8745 (tt) cc_final: 0.8320 (tt) REVERT: e 65 SER cc_start: 0.8894 (t) cc_final: 0.8500 (p) REVERT: g 42 MET cc_start: 0.8524 (tmm) cc_final: 0.7217 (tpt) REVERT: h 6 ASP cc_start: 0.5202 (p0) cc_final: 0.4264 (m-30) REVERT: h 9 LYS cc_start: 0.8180 (tttt) cc_final: 0.7952 (ttpp) REVERT: h 41 TYR cc_start: 0.8704 (t80) cc_final: 0.8495 (t80) REVERT: h 43 MET cc_start: 0.7787 (mtm) cc_final: 0.7586 (mtm) REVERT: h 49 PHE cc_start: 0.8903 (m-80) cc_final: 0.8455 (m-80) REVERT: i 9 LYS cc_start: 0.8357 (tttt) cc_final: 0.8112 (tptt) REVERT: i 41 TYR cc_start: 0.8429 (t80) cc_final: 0.8221 (t80) REVERT: j 12 ASP cc_start: 0.8589 (p0) cc_final: 0.8091 (m-30) REVERT: j 39 ILE cc_start: 0.9595 (tp) cc_final: 0.9211 (tp) REVERT: j 42 MET cc_start: 0.9099 (tmm) cc_final: 0.8541 (tmm) REVERT: j 58 THR cc_start: 0.8753 (m) cc_final: 0.8552 (p) REVERT: l 42 MET cc_start: 0.9184 (tmm) cc_final: 0.8780 (tmm) REVERT: m 41 TYR cc_start: 0.8455 (t80) cc_final: 0.8179 (t80) REVERT: m 64 MET cc_start: 0.8428 (mmt) cc_final: 0.7965 (mmt) REVERT: n 40 MET cc_start: 0.8481 (mmp) cc_final: 0.8076 (mmt) REVERT: n 65 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8218 (p) REVERT: o 9 LYS cc_start: 0.8360 (tttt) cc_final: 0.8078 (ttpt) outliers start: 81 outliers final: 39 residues processed: 771 average time/residue: 0.3058 time to fit residues: 383.5219 Evaluate side-chains 670 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 628 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 K residue 60 ILE Chi-restraints excluded: chain L residue 26 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 Q residue 65 SER Chi-restraints excluded: chain R residue 8 MET Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 10 SER 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 b residue 34 VAL 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 f residue 7 LEU Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 29 VAL 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 j residue 34 VAL 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 47 VAL 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 157 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 245 optimal weight: 0.8980 chunk 218 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 223 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109605 restraints weight = 29066.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113176 restraints weight = 13639.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.115239 restraints weight = 7424.913| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22427 Z= 0.135 Angle : 0.591 9.801 29725 Z= 0.305 Chirality : 0.040 0.204 3403 Planarity : 0.003 0.017 3321 Dihedral : 14.866 89.943 4633 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.89 % Allowed : 18.81 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.16), residues: 2624 helix: 1.56 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.33 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 28 PHE 0.019 0.001 PHE C 49 TYR 0.014 0.001 TYR f 41 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 1681) hydrogen bonds : angle 5.63114 ( 5043) covalent geometry : bond 0.00276 (22427) covalent geometry : angle 0.59087 (29725) *********************** 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 743 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 660 time to evaluate : 2.409 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8745 (tttt) cc_final: 0.8505 (tttp) REVERT: B 9 LYS cc_start: 0.8853 (tttt) cc_final: 0.8491 (ttpp) REVERT: C 64 MET cc_start: 0.9204 (tpp) cc_final: 0.9001 (mmt) REVERT: D 9 LYS cc_start: 0.8776 (tttt) cc_final: 0.8476 (ttpp) REVERT: G 21 LYS cc_start: 0.8274 (tttt) cc_final: 0.8045 (tttm) REVERT: G 23 SER cc_start: 0.8653 (p) cc_final: 0.8362 (p) REVERT: G 41 TYR cc_start: 0.8277 (t80) cc_final: 0.8056 (t80) REVERT: G 64 MET cc_start: 0.8957 (mmt) cc_final: 0.8637 (mmm) REVERT: H 41 TYR cc_start: 0.8426 (t80) cc_final: 0.8211 (t80) REVERT: H 42 MET cc_start: 0.9204 (tmm) cc_final: 0.8905 (tmm) REVERT: L 65 SER cc_start: 0.9261 (t) cc_final: 0.9052 (p) REVERT: N 8 MET cc_start: 0.7214 (tpp) cc_final: 0.6991 (tpt) REVERT: N 65 SER cc_start: 0.9067 (t) cc_final: 0.8708 (p) REVERT: O 42 MET cc_start: 0.8791 (tmm) cc_final: 0.8140 (tmm) REVERT: O 43 MET cc_start: 0.8073 (mtm) cc_final: 0.7603 (mtp) REVERT: Q 41 TYR cc_start: 0.8902 (t80) cc_final: 0.8581 (t80) REVERT: R 5 THR cc_start: 0.7072 (p) cc_final: 0.6559 (t) REVERT: R 8 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6979 (tpp) REVERT: R 64 MET cc_start: 0.8948 (mmm) cc_final: 0.8672 (mmm) REVERT: S 21 LYS cc_start: 0.8255 (tptm) cc_final: 0.7854 (tptm) REVERT: S 22 GLN cc_start: 0.8098 (mp10) cc_final: 0.7868 (pm20) REVERT: T 42 MET cc_start: 0.8435 (ttp) cc_final: 0.8108 (tmm) REVERT: U 9 LYS cc_start: 0.7855 (ttpp) cc_final: 0.7550 (ttpt) REVERT: X 40 MET cc_start: 0.8510 (mmm) cc_final: 0.8295 (mmm) REVERT: X 46 ASN cc_start: 0.8561 (t0) cc_final: 0.8098 (t0) REVERT: Y 41 TYR cc_start: 0.8776 (t80) cc_final: 0.8488 (t80) REVERT: Y 64 MET cc_start: 0.8556 (mmt) cc_final: 0.8172 (mmt) REVERT: Z 41 TYR cc_start: 0.9013 (t80) cc_final: 0.8587 (t80) REVERT: a 8 MET cc_start: 0.7393 (tpp) cc_final: 0.7136 (tpp) REVERT: a 41 TYR cc_start: 0.8768 (t80) cc_final: 0.8547 (t80) REVERT: e 65 SER cc_start: 0.9023 (t) cc_final: 0.8699 (p) REVERT: g 42 MET cc_start: 0.8252 (tmm) cc_final: 0.7158 (tpt) REVERT: h 6 ASP cc_start: 0.5354 (p0) cc_final: 0.4402 (m-30) REVERT: h 15 VAL cc_start: 0.8621 (m) cc_final: 0.8273 (p) REVERT: i 41 TYR cc_start: 0.8229 (t80) cc_final: 0.8018 (t80) REVERT: j 42 MET cc_start: 0.9050 (tmm) cc_final: 0.8474 (tmm) REVERT: j 58 THR cc_start: 0.8876 (m) cc_final: 0.8558 (p) REVERT: m 64 MET cc_start: 0.8682 (mmt) cc_final: 0.8173 (mmt) REVERT: n 40 MET cc_start: 0.8333 (mmp) cc_final: 0.8052 (mmt) outliers start: 83 outliers final: 54 residues processed: 704 average time/residue: 0.2929 time to fit residues: 331.4459 Evaluate side-chains 651 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 596 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain R residue 8 MET Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 62 ILE Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 58 THR 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 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain c residue 44 THR 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 60 ILE Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain k residue 7 LEU 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 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 179 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** g 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3346 r_free = 0.3346 target = 0.123880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.108293 restraints weight = 29516.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111776 restraints weight = 13900.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113869 restraints weight = 7642.024| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22427 Z= 0.133 Angle : 0.593 9.260 29725 Z= 0.301 Chirality : 0.040 0.184 3403 Planarity : 0.002 0.017 3321 Dihedral : 14.476 88.497 4633 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 3.99 % Allowed : 20.36 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.17), residues: 2624 helix: 1.72 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 1.71 (0.34), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 28 PHE 0.017 0.001 PHE h 49 TYR 0.012 0.001 TYR X 41 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 1681) hydrogen bonds : angle 5.45089 ( 5043) covalent geometry : bond 0.00275 (22427) covalent geometry : angle 0.59285 (29725) *********************** 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 716 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 631 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8971 (tttt) cc_final: 0.8765 (tttm) REVERT: C 64 MET cc_start: 0.9337 (tpp) cc_final: 0.9063 (mmt) REVERT: D 9 LYS cc_start: 0.8780 (tttt) cc_final: 0.8489 (ttpp) REVERT: G 21 LYS cc_start: 0.8134 (tttt) cc_final: 0.7683 (tptt) REVERT: G 64 MET cc_start: 0.8969 (mmt) cc_final: 0.8710 (mmm) REVERT: H 41 TYR cc_start: 0.8527 (t80) cc_final: 0.8272 (t80) REVERT: H 42 MET cc_start: 0.9175 (tmm) cc_final: 0.8889 (tmm) REVERT: L 42 MET cc_start: 0.8696 (tmm) cc_final: 0.8438 (tmm) REVERT: M 12 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8682 (t0) REVERT: M 62 ILE cc_start: 0.7972 (mm) cc_final: 0.7662 (mt) REVERT: N 40 MET cc_start: 0.8575 (tpp) cc_final: 0.8326 (tpp) REVERT: N 41 TYR cc_start: 0.8913 (t80) cc_final: 0.8700 (t80) REVERT: N 62 ILE cc_start: 0.8749 (mm) cc_final: 0.8484 (mt) REVERT: N 65 SER cc_start: 0.9027 (t) cc_final: 0.8732 (p) REVERT: O 42 MET cc_start: 0.8842 (tmm) cc_final: 0.8607 (tmm) REVERT: Q 8 MET cc_start: 0.7983 (tpp) cc_final: 0.7575 (mpp) REVERT: R 5 THR cc_start: 0.7152 (p) cc_final: 0.6528 (t) REVERT: R 8 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: R 64 MET cc_start: 0.8908 (mmm) cc_final: 0.8614 (mmm) REVERT: S 21 LYS cc_start: 0.8166 (tptm) cc_final: 0.7934 (tptm) REVERT: S 22 GLN cc_start: 0.8000 (mp10) cc_final: 0.7799 (pm20) REVERT: T 42 MET cc_start: 0.8553 (ttp) cc_final: 0.8224 (tmm) REVERT: U 8 MET cc_start: 0.7813 (mmm) cc_final: 0.7396 (tpp) REVERT: U 64 MET cc_start: 0.8497 (mmt) cc_final: 0.8282 (mmm) REVERT: W 56 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8250 (mt) REVERT: Y 64 MET cc_start: 0.8534 (mmt) cc_final: 0.8173 (mmt) REVERT: Z 8 MET cc_start: 0.7497 (tpp) cc_final: 0.7147 (mmm) REVERT: Z 41 TYR cc_start: 0.8935 (t80) cc_final: 0.8574 (t80) REVERT: a 41 TYR cc_start: 0.8725 (t80) cc_final: 0.8488 (t80) REVERT: c 64 MET cc_start: 0.8598 (mmt) cc_final: 0.7964 (mmm) REVERT: d 8 MET cc_start: 0.7946 (mmm) cc_final: 0.7635 (mmm) REVERT: e 44 THR cc_start: 0.9225 (m) cc_final: 0.8941 (m) REVERT: e 65 SER cc_start: 0.8986 (t) cc_final: 0.8723 (p) REVERT: g 42 MET cc_start: 0.8085 (tmm) cc_final: 0.7143 (tpt) REVERT: h 15 VAL cc_start: 0.8907 (m) cc_final: 0.8630 (p) REVERT: h 21 LYS cc_start: 0.8092 (tttt) cc_final: 0.7661 (tptm) REVERT: i 41 TYR cc_start: 0.8322 (t80) cc_final: 0.8058 (t80) REVERT: j 42 MET cc_start: 0.8927 (tmm) cc_final: 0.8325 (tmm) REVERT: l 42 MET cc_start: 0.9106 (tmm) cc_final: 0.8760 (tmm) REVERT: m 8 MET cc_start: 0.7624 (tpp) cc_final: 0.7381 (tpp) REVERT: m 64 MET cc_start: 0.8714 (mmt) cc_final: 0.8184 (mmt) REVERT: n 8 MET cc_start: 0.7418 (tpt) cc_final: 0.5698 (ptm) REVERT: n 40 MET cc_start: 0.8371 (mmp) cc_final: 0.8137 (mmt) outliers start: 85 outliers final: 63 residues processed: 689 average time/residue: 0.2938 time to fit residues: 326.8931 Evaluate side-chains 646 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 580 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain R residue 8 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 47 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 30 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 55 ILE 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 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain i residue 7 LEU Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU 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 35 VAL Chi-restraints excluded: chain l residue 55 ILE Chi-restraints excluded: chain m residue 60 ILE 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 137 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3292 r_free = 0.3292 target = 0.120037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.104124 restraints weight = 29944.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107567 restraints weight = 14241.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.109665 restraints weight = 7882.716| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22427 Z= 0.154 Angle : 0.612 9.766 29725 Z= 0.311 Chirality : 0.040 0.232 3403 Planarity : 0.003 0.017 3321 Dihedral : 14.327 89.995 4633 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.13 % Allowed : 20.17 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.16), residues: 2624 helix: 1.77 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.99 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 28 PHE 0.025 0.001 PHE h 49 TYR 0.016 0.001 TYR C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 1681) hydrogen bonds : angle 5.38472 ( 5043) covalent geometry : bond 0.00340 (22427) covalent geometry : angle 0.61184 (29725) *********************** 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 697 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 609 time to evaluate : 2.413 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.9034 (tttt) cc_final: 0.8819 (tttp) REVERT: D 9 LYS cc_start: 0.8874 (tttt) cc_final: 0.8494 (ttpp) REVERT: G 21 LYS cc_start: 0.8184 (tttt) cc_final: 0.7759 (tptt) REVERT: G 23 SER cc_start: 0.8858 (p) cc_final: 0.8532 (p) REVERT: G 41 TYR cc_start: 0.8491 (t80) cc_final: 0.7893 (t80) REVERT: G 64 MET cc_start: 0.9051 (mmt) cc_final: 0.8751 (mmm) REVERT: H 41 TYR cc_start: 0.8695 (t80) cc_final: 0.8357 (t80) REVERT: H 42 MET cc_start: 0.9112 (tmm) cc_final: 0.8819 (tmm) REVERT: K 41 TYR cc_start: 0.8822 (t80) cc_final: 0.8226 (t80) REVERT: L 41 TYR cc_start: 0.8769 (t80) cc_final: 0.8149 (t80) REVERT: L 42 MET cc_start: 0.8576 (tmm) cc_final: 0.8316 (tmm) REVERT: L 64 MET cc_start: 0.8453 (mmm) cc_final: 0.8047 (mmm) REVERT: M 12 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8747 (t0) REVERT: M 62 ILE cc_start: 0.7980 (mm) cc_final: 0.7765 (mt) REVERT: N 62 ILE cc_start: 0.8907 (mm) cc_final: 0.8693 (mm) REVERT: N 64 MET cc_start: 0.8737 (mmm) cc_final: 0.8474 (mmm) REVERT: N 65 SER cc_start: 0.9066 (t) cc_final: 0.8717 (p) REVERT: P 41 TYR cc_start: 0.8943 (t80) cc_final: 0.8734 (t80) REVERT: P 62 ILE cc_start: 0.8797 (mm) cc_final: 0.8494 (mm) REVERT: R 5 THR cc_start: 0.7175 (p) cc_final: 0.6622 (t) REVERT: R 64 MET cc_start: 0.8930 (mmm) cc_final: 0.8618 (mmm) REVERT: T 42 MET cc_start: 0.8626 (ttp) cc_final: 0.8212 (tmm) REVERT: U 8 MET cc_start: 0.7900 (mmm) cc_final: 0.7682 (tpp) REVERT: W 40 MET cc_start: 0.7946 (mmt) cc_final: 0.7705 (tpp) REVERT: X 40 MET cc_start: 0.8897 (mmm) cc_final: 0.8689 (mmm) REVERT: Y 64 MET cc_start: 0.8443 (mmt) cc_final: 0.8142 (mmm) REVERT: Z 40 MET cc_start: 0.8414 (mmm) cc_final: 0.8104 (mmm) REVERT: Z 64 MET cc_start: 0.9004 (mmt) cc_final: 0.8423 (mmt) REVERT: a 41 TYR cc_start: 0.8852 (t80) cc_final: 0.8468 (t80) REVERT: c 64 MET cc_start: 0.8684 (mmt) cc_final: 0.8161 (mmm) REVERT: d 8 MET cc_start: 0.7927 (mmm) cc_final: 0.7644 (mmm) REVERT: d 22 GLN cc_start: 0.7777 (mp10) cc_final: 0.7344 (mp10) REVERT: e 65 SER cc_start: 0.9043 (t) cc_final: 0.8744 (p) REVERT: f 9 LYS cc_start: 0.8154 (tttp) cc_final: 0.7497 (tppt) REVERT: g 9 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7823 (ttpp) REVERT: h 21 LYS cc_start: 0.8164 (tttt) cc_final: 0.7706 (tptm) REVERT: j 12 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8120 (t0) REVERT: j 42 MET cc_start: 0.8977 (tmm) cc_final: 0.8372 (tmm) REVERT: l 50 LEU cc_start: 0.9283 (mt) cc_final: 0.8918 (mt) REVERT: m 8 MET cc_start: 0.7508 (tpp) cc_final: 0.7285 (tpp) REVERT: m 64 MET cc_start: 0.8738 (mmt) cc_final: 0.8438 (mmt) REVERT: n 8 MET cc_start: 0.7380 (tpt) cc_final: 0.5795 (ptt) REVERT: n 40 MET cc_start: 0.8240 (mmp) cc_final: 0.7876 (mmt) outliers start: 88 outliers final: 68 residues processed: 670 average time/residue: 0.2901 time to fit residues: 314.3376 Evaluate side-chains 644 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 574 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 9 LYS Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M 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 P residue 60 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 44 THR 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 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 12 ASP 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 35 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 50 optimal weight: 2.9990 chunk 222 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.119496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103535 restraints weight = 29573.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.106838 restraints weight = 14042.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.108858 restraints weight = 7840.863| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22427 Z= 0.153 Angle : 0.628 10.220 29725 Z= 0.315 Chirality : 0.040 0.221 3403 Planarity : 0.002 0.014 3321 Dihedral : 14.371 89.176 4633 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 4.46 % Allowed : 21.01 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.16), residues: 2624 helix: 1.77 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.71 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 28 PHE 0.021 0.001 PHE C 53 TYR 0.015 0.001 TYR f 41 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 1681) hydrogen bonds : angle 5.32645 ( 5043) covalent geometry : bond 0.00348 (22427) covalent geometry : angle 0.62818 (29725) *********************** 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: 95 poor density : 608 time to evaluate : 2.035 Fit side-chains REVERT: D 9 LYS cc_start: 0.8915 (tttt) cc_final: 0.8520 (ttpp) REVERT: E 23 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8632 (p) REVERT: F 9 LYS cc_start: 0.8831 (tppt) cc_final: 0.8579 (tppt) REVERT: G 21 LYS cc_start: 0.8199 (tttt) cc_final: 0.7928 (tptt) REVERT: G 23 SER cc_start: 0.8891 (p) cc_final: 0.8516 (p) REVERT: G 41 TYR cc_start: 0.8491 (t80) cc_final: 0.7963 (t80) REVERT: H 41 TYR cc_start: 0.8772 (t80) cc_final: 0.8376 (t80) REVERT: H 42 MET cc_start: 0.9188 (tmm) cc_final: 0.8928 (tmm) REVERT: L 41 TYR cc_start: 0.8757 (t80) cc_final: 0.8005 (t80) REVERT: L 42 MET cc_start: 0.8539 (tmm) cc_final: 0.8240 (tmm) REVERT: L 64 MET cc_start: 0.8542 (mmm) cc_final: 0.8172 (mmm) REVERT: M 8 MET cc_start: 0.8509 (mmt) cc_final: 0.8221 (mtt) REVERT: M 9 LYS cc_start: 0.8254 (ttpt) cc_final: 0.8043 (mtmm) REVERT: M 12 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8754 (t0) REVERT: N 62 ILE cc_start: 0.8932 (mm) cc_final: 0.8702 (mm) REVERT: N 65 SER cc_start: 0.9034 (t) cc_final: 0.8689 (p) REVERT: R 64 MET cc_start: 0.8919 (mmm) cc_final: 0.8581 (mmm) REVERT: S 42 MET cc_start: 0.8589 (tmm) cc_final: 0.8138 (tmm) REVERT: T 5 THR cc_start: 0.6582 (p) cc_final: 0.5725 (t) REVERT: T 42 MET cc_start: 0.8635 (ttp) cc_final: 0.8210 (tmm) REVERT: U 64 MET cc_start: 0.8654 (mmt) cc_final: 0.8199 (mmt) REVERT: W 40 MET cc_start: 0.7971 (mmt) cc_final: 0.7732 (tpp) REVERT: X 40 MET cc_start: 0.8999 (mmm) cc_final: 0.8765 (mmm) REVERT: Y 41 TYR cc_start: 0.8870 (t80) cc_final: 0.8616 (t80) REVERT: Y 64 MET cc_start: 0.8421 (mmt) cc_final: 0.8153 (mmt) REVERT: Z 8 MET cc_start: 0.7890 (mmm) cc_final: 0.7679 (mpp) REVERT: Z 9 LYS cc_start: 0.8291 (tttt) cc_final: 0.7981 (tppt) REVERT: Z 64 MET cc_start: 0.8983 (mmt) cc_final: 0.8771 (mmm) REVERT: a 8 MET cc_start: 0.7823 (tpp) cc_final: 0.7507 (tpp) REVERT: c 64 MET cc_start: 0.8764 (mmt) cc_final: 0.8249 (mmm) REVERT: d 8 MET cc_start: 0.7948 (mmm) cc_final: 0.7721 (mmm) REVERT: d 22 GLN cc_start: 0.7805 (mp10) cc_final: 0.7429 (mp10) REVERT: d 33 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8042 (tm-30) REVERT: e 65 SER cc_start: 0.9037 (t) cc_final: 0.8759 (p) REVERT: f 9 LYS cc_start: 0.8195 (tttp) cc_final: 0.7445 (tppt) REVERT: f 21 LYS cc_start: 0.8041 (tttt) cc_final: 0.7519 (tptm) REVERT: g 42 MET cc_start: 0.8385 (tmm) cc_final: 0.7233 (tpt) REVERT: g 65 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8665 (m) REVERT: j 12 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: j 42 MET cc_start: 0.9069 (tmm) cc_final: 0.8338 (tmm) REVERT: j 55 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8691 (pt) REVERT: l 42 MET cc_start: 0.9042 (tmm) cc_final: 0.8626 (tmm) REVERT: l 50 LEU cc_start: 0.9275 (mt) cc_final: 0.8905 (mt) REVERT: m 8 MET cc_start: 0.7506 (tpp) cc_final: 0.7184 (tpp) REVERT: m 64 MET cc_start: 0.8729 (mmt) cc_final: 0.8415 (mmp) REVERT: n 8 MET cc_start: 0.7256 (tpt) cc_final: 0.5660 (ptt) REVERT: n 40 MET cc_start: 0.8179 (mmp) cc_final: 0.7877 (mmt) REVERT: n 42 MET cc_start: 0.7851 (tmm) cc_final: 0.7351 (tmm) outliers start: 95 outliers final: 73 residues processed: 669 average time/residue: 0.2821 time to fit residues: 304.6830 Evaluate side-chains 646 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 568 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 34 VAL 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 J residue 56 ILE Chi-restraints excluded: chain K residue 56 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 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain O residue 10 SER 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 Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 THR 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 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 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 12 ASP Chi-restraints excluded: chain j residue 55 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 35 VAL Chi-restraints excluded: chain l residue 39 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 29 VAL Chi-restraints excluded: chain o residue 56 ILE Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 1 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 210 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.116020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100466 restraints weight = 30162.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103533 restraints weight = 14670.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.105470 restraints weight = 8341.139| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22427 Z= 0.179 Angle : 0.664 11.167 29725 Z= 0.335 Chirality : 0.042 0.244 3403 Planarity : 0.003 0.015 3321 Dihedral : 14.682 88.030 4633 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.03 % Allowed : 22.47 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.16), residues: 2624 helix: 1.63 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.68 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 28 PHE 0.028 0.001 PHE C 53 TYR 0.014 0.002 TYR f 41 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 1681) hydrogen bonds : angle 5.32893 ( 5043) covalent geometry : bond 0.00417 (22427) covalent geometry : angle 0.66415 (29725) *********************** 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: 86 poor density : 608 time to evaluate : 2.182 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.8997 (tttm) cc_final: 0.8795 (tttp) REVERT: B 12 ASP cc_start: 0.8652 (m-30) cc_final: 0.8342 (t0) REVERT: C 33 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 64 MET cc_start: 0.9018 (mmt) cc_final: 0.8481 (mmm) REVERT: D 9 LYS cc_start: 0.8909 (tttt) cc_final: 0.8551 (ttpp) REVERT: G 21 LYS cc_start: 0.8387 (tttt) cc_final: 0.8105 (tptt) REVERT: G 41 TYR cc_start: 0.8487 (t80) cc_final: 0.8082 (t80) REVERT: H 41 TYR cc_start: 0.8754 (t80) cc_final: 0.8541 (t80) REVERT: H 42 MET cc_start: 0.9151 (tmm) cc_final: 0.8918 (tmm) REVERT: L 41 TYR cc_start: 0.8774 (t80) cc_final: 0.7919 (t80) REVERT: L 42 MET cc_start: 0.8476 (tmm) cc_final: 0.8240 (tmm) REVERT: L 64 MET cc_start: 0.8647 (mmm) cc_final: 0.8248 (mmm) REVERT: N 64 MET cc_start: 0.8711 (mmm) cc_final: 0.8463 (mmm) REVERT: N 65 SER cc_start: 0.9016 (t) cc_final: 0.8714 (p) REVERT: P 40 MET cc_start: 0.8430 (mmm) cc_final: 0.8186 (mmm) REVERT: R 5 THR cc_start: 0.6857 (p) cc_final: 0.6370 (t) REVERT: R 64 MET cc_start: 0.8845 (mmm) cc_final: 0.8466 (mmm) REVERT: U 64 MET cc_start: 0.8606 (mmt) cc_final: 0.8178 (mmt) REVERT: Y 64 MET cc_start: 0.8367 (mmt) cc_final: 0.8066 (mmm) REVERT: Z 9 LYS cc_start: 0.8416 (tttt) cc_final: 0.8184 (tppt) REVERT: Z 40 MET cc_start: 0.8259 (mmm) cc_final: 0.7947 (mmm) REVERT: a 8 MET cc_start: 0.7986 (tpp) cc_final: 0.7612 (tpp) REVERT: d 22 GLN cc_start: 0.7820 (mp10) cc_final: 0.7506 (mp10) REVERT: e 40 MET cc_start: 0.7527 (tpp) cc_final: 0.7283 (tpp) REVERT: e 65 SER cc_start: 0.9025 (t) cc_final: 0.8729 (p) REVERT: f 9 LYS cc_start: 0.8313 (tttp) cc_final: 0.7605 (tppt) REVERT: f 21 LYS cc_start: 0.8112 (tttt) cc_final: 0.7440 (tptt) REVERT: f 31 LEU cc_start: 0.8925 (tp) cc_final: 0.8668 (tt) REVERT: f 58 THR cc_start: 0.8882 (m) cc_final: 0.8603 (p) REVERT: h 42 MET cc_start: 0.8753 (tmm) cc_final: 0.8519 (tmm) REVERT: j 42 MET cc_start: 0.9011 (tmm) cc_final: 0.8277 (tmm) REVERT: j 55 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8728 (pt) REVERT: l 50 LEU cc_start: 0.9267 (mt) cc_final: 0.8909 (mt) REVERT: m 64 MET cc_start: 0.8744 (mmt) cc_final: 0.8445 (mmt) REVERT: n 8 MET cc_start: 0.7222 (tpt) cc_final: 0.5753 (ptt) REVERT: n 40 MET cc_start: 0.8200 (mmp) cc_final: 0.7917 (mmt) REVERT: n 42 MET cc_start: 0.7822 (tmm) cc_final: 0.7440 (tmm) outliers start: 86 outliers final: 74 residues processed: 667 average time/residue: 0.3093 time to fit residues: 333.0533 Evaluate side-chains 639 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 564 time to evaluate : 2.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 60 ILE 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 F residue 34 VAL Chi-restraints excluded: chain G residue 6 ASP 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 J residue 56 ILE Chi-restraints excluded: chain K residue 56 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 12 ASP Chi-restraints excluded: chain M 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 P residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 60 ILE 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 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 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 55 ILE 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 35 VAL Chi-restraints excluded: chain l residue 39 ILE Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 60 ILE 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 18 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.122614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.106892 restraints weight = 29641.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.110287 restraints weight = 14048.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.112404 restraints weight = 7807.217| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.6616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22427 Z= 0.134 Angle : 0.654 13.074 29725 Z= 0.323 Chirality : 0.039 0.253 3403 Planarity : 0.003 0.023 3321 Dihedral : 14.347 89.973 4633 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.72 % Allowed : 24.72 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.16), residues: 2624 helix: 1.83 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 0.25 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 28 PHE 0.025 0.001 PHE j 49 TYR 0.016 0.001 TYR f 41 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1681) hydrogen bonds : angle 5.24711 ( 5043) covalent geometry : bond 0.00296 (22427) covalent geometry : angle 0.65425 (29725) *********************** 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 672 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 614 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.8979 (mmt) cc_final: 0.8497 (mmm) REVERT: D 9 LYS cc_start: 0.8852 (tttt) cc_final: 0.8512 (ttpp) REVERT: E 23 SER cc_start: 0.8805 (p) cc_final: 0.8544 (p) REVERT: G 21 LYS cc_start: 0.8354 (tttt) cc_final: 0.8028 (tptt) REVERT: G 41 TYR cc_start: 0.8409 (t80) cc_final: 0.7911 (t80) REVERT: H 16 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8624 (ttpt) REVERT: H 19 PHE cc_start: 0.8859 (m-80) cc_final: 0.8649 (m-10) REVERT: H 41 TYR cc_start: 0.8712 (t80) cc_final: 0.8475 (t80) REVERT: L 41 TYR cc_start: 0.8752 (t80) cc_final: 0.8063 (t80) REVERT: L 42 MET cc_start: 0.8523 (tmm) cc_final: 0.8226 (tmm) REVERT: L 64 MET cc_start: 0.8486 (mmm) cc_final: 0.8150 (mmm) REVERT: M 12 ASP cc_start: 0.8994 (OUTLIER) cc_final: 0.8725 (t0) REVERT: N 64 MET cc_start: 0.8593 (mmm) cc_final: 0.8372 (mmm) REVERT: N 65 SER cc_start: 0.8929 (t) cc_final: 0.8678 (p) REVERT: O 41 TYR cc_start: 0.9173 (t80) cc_final: 0.8882 (t80) REVERT: R 5 THR cc_start: 0.6490 (p) cc_final: 0.6023 (t) REVERT: R 64 MET cc_start: 0.8859 (mmm) cc_final: 0.8643 (mmm) REVERT: S 21 LYS cc_start: 0.8539 (tptm) cc_final: 0.7825 (tptp) REVERT: W 41 TYR cc_start: 0.8877 (t80) cc_final: 0.8585 (t80) REVERT: Y 41 TYR cc_start: 0.8889 (t80) cc_final: 0.8637 (t80) REVERT: Y 64 MET cc_start: 0.8304 (mmt) cc_final: 0.8058 (mmt) REVERT: Z 9 LYS cc_start: 0.8454 (tttt) cc_final: 0.8193 (tppt) REVERT: Z 40 MET cc_start: 0.8326 (mmm) cc_final: 0.7974 (mmm) REVERT: a 8 MET cc_start: 0.7818 (tpp) cc_final: 0.7464 (tpp) REVERT: c 64 MET cc_start: 0.8679 (mmt) cc_final: 0.8199 (mmm) REVERT: d 22 GLN cc_start: 0.7806 (mp10) cc_final: 0.7454 (mp10) REVERT: e 12 ASP cc_start: 0.8220 (p0) cc_final: 0.7784 (t0) REVERT: e 15 VAL cc_start: 0.9296 (t) cc_final: 0.8975 (p) REVERT: e 40 MET cc_start: 0.7499 (tpp) cc_final: 0.7270 (tpp) REVERT: e 65 SER cc_start: 0.9014 (t) cc_final: 0.8794 (p) REVERT: f 9 LYS cc_start: 0.8311 (tttp) cc_final: 0.7749 (tppt) REVERT: f 21 LYS cc_start: 0.8127 (tttt) cc_final: 0.7397 (tptt) REVERT: f 41 TYR cc_start: 0.8999 (t80) cc_final: 0.8631 (t80) REVERT: f 48 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7890 (ptpt) REVERT: f 58 THR cc_start: 0.8883 (m) cc_final: 0.8584 (p) REVERT: g 42 MET cc_start: 0.8358 (tmm) cc_final: 0.7165 (tpt) REVERT: h 49 PHE cc_start: 0.8659 (m-10) cc_final: 0.8367 (m-10) REVERT: j 42 MET cc_start: 0.9045 (tmm) cc_final: 0.8111 (tmm) REVERT: j 55 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8624 (pt) REVERT: l 50 LEU cc_start: 0.9228 (mt) cc_final: 0.8879 (mt) REVERT: m 64 MET cc_start: 0.8665 (mmt) cc_final: 0.8450 (mmp) REVERT: n 8 MET cc_start: 0.7240 (tpt) cc_final: 0.5834 (ptt) REVERT: n 40 MET cc_start: 0.8052 (mmp) cc_final: 0.7789 (mmt) REVERT: n 42 MET cc_start: 0.7690 (tmm) cc_final: 0.7437 (tmm) outliers start: 58 outliers final: 45 residues processed: 657 average time/residue: 0.3116 time to fit residues: 331.2294 Evaluate side-chains 624 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 576 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain G residue 7 LEU 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 56 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 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X 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 d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 48 LYS Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 23 SER 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 55 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 120 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.114914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.098981 restraints weight = 30769.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.102147 restraints weight = 14811.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.104101 restraints weight = 8365.846| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22427 Z= 0.205 Angle : 0.745 12.699 29725 Z= 0.368 Chirality : 0.043 0.304 3403 Planarity : 0.003 0.028 3321 Dihedral : 14.915 87.955 4633 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.56 % Allowed : 24.25 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.16), residues: 2624 helix: 1.63 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.43 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 28 PHE 0.029 0.002 PHE C 53 TYR 0.027 0.002 TYR c 41 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 1681) hydrogen bonds : angle 5.28808 ( 5043) covalent geometry : bond 0.00488 (22427) covalent geometry : angle 0.74501 (29725) *********************** 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 652 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 576 time to evaluate : 2.979 Fit side-chains REVERT: B 12 ASP cc_start: 0.8724 (m-30) cc_final: 0.8358 (t0) REVERT: C 64 MET cc_start: 0.9055 (mmt) cc_final: 0.8559 (mmm) REVERT: D 9 LYS cc_start: 0.8906 (tttt) cc_final: 0.8545 (ttpp) REVERT: E 23 SER cc_start: 0.9039 (p) cc_final: 0.8806 (p) REVERT: G 21 LYS cc_start: 0.8381 (tttt) cc_final: 0.8132 (tptt) REVERT: G 41 TYR cc_start: 0.8552 (t80) cc_final: 0.8081 (t80) REVERT: G 43 MET cc_start: 0.7964 (mtp) cc_final: 0.7747 (mtp) REVERT: I 41 TYR cc_start: 0.8768 (t80) cc_final: 0.8471 (t80) REVERT: K 41 TYR cc_start: 0.8923 (t80) cc_final: 0.8409 (t80) REVERT: L 41 TYR cc_start: 0.8809 (t80) cc_final: 0.7886 (t80) REVERT: L 42 MET cc_start: 0.8449 (tmm) cc_final: 0.8207 (tmm) REVERT: L 64 MET cc_start: 0.8720 (mmm) cc_final: 0.8344 (mmm) REVERT: N 64 MET cc_start: 0.8748 (mmm) cc_final: 0.8488 (mmm) REVERT: N 65 SER cc_start: 0.9070 (t) cc_final: 0.8692 (p) REVERT: R 64 MET cc_start: 0.8893 (mmm) cc_final: 0.8543 (mmm) REVERT: S 26 VAL cc_start: 0.8699 (m) cc_final: 0.8421 (t) REVERT: S 42 MET cc_start: 0.8466 (tmm) cc_final: 0.8133 (tmm) REVERT: T 6 ASP cc_start: 0.6170 (p0) cc_final: 0.5921 (p0) REVERT: V 5 THR cc_start: 0.6595 (p) cc_final: 0.6260 (t) REVERT: W 21 LYS cc_start: 0.8582 (tptm) cc_final: 0.8259 (tptp) REVERT: Y 64 MET cc_start: 0.8322 (mmt) cc_final: 0.8044 (mmm) REVERT: Z 9 LYS cc_start: 0.8539 (tttt) cc_final: 0.8177 (tppt) REVERT: Z 22 GLN cc_start: 0.7841 (pm20) cc_final: 0.7540 (mt0) REVERT: Z 40 MET cc_start: 0.8440 (mmm) cc_final: 0.8158 (mmm) REVERT: Z 64 MET cc_start: 0.9070 (mmt) cc_final: 0.8844 (mmm) REVERT: a 8 MET cc_start: 0.8060 (tpp) cc_final: 0.7698 (tpp) REVERT: b 22 GLN cc_start: 0.7845 (pm20) cc_final: 0.7470 (mt0) REVERT: d 22 GLN cc_start: 0.7953 (mp10) cc_final: 0.7706 (mp10) REVERT: e 15 VAL cc_start: 0.9309 (t) cc_final: 0.8953 (p) REVERT: e 40 MET cc_start: 0.7728 (tpp) cc_final: 0.7394 (tpp) REVERT: e 65 SER cc_start: 0.9072 (t) cc_final: 0.8794 (p) REVERT: f 9 LYS cc_start: 0.8432 (tttp) cc_final: 0.7839 (tppt) REVERT: f 58 THR cc_start: 0.8893 (m) cc_final: 0.8598 (p) REVERT: f 59 PHE cc_start: 0.8305 (t80) cc_final: 0.8041 (t80) REVERT: h 49 PHE cc_start: 0.8792 (m-10) cc_final: 0.8562 (m-10) REVERT: j 42 MET cc_start: 0.8912 (tmm) cc_final: 0.8698 (tmm) REVERT: j 55 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8710 (pt) REVERT: l 42 MET cc_start: 0.9017 (tmm) cc_final: 0.8553 (tmm) REVERT: l 50 LEU cc_start: 0.9274 (mt) cc_final: 0.8928 (mt) REVERT: m 64 MET cc_start: 0.8737 (mmt) cc_final: 0.8464 (mmt) REVERT: n 8 MET cc_start: 0.7181 (tpt) cc_final: 0.5753 (ptt) REVERT: n 42 MET cc_start: 0.7760 (tmm) cc_final: 0.7353 (tmm) outliers start: 76 outliers final: 61 residues processed: 634 average time/residue: 0.3049 time to fit residues: 311.4630 Evaluate side-chains 619 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 557 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE 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 C residue 60 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 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 7 LEU Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain O residue 10 SER 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 P residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X 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 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 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 34 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 8 MET Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 57 SER Chi-restraints excluded: chain m residue 60 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 109 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.117345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101248 restraints weight = 30435.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.104504 restraints weight = 14623.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106518 restraints weight = 8202.660| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22427 Z= 0.174 Angle : 0.747 16.834 29725 Z= 0.365 Chirality : 0.041 0.275 3403 Planarity : 0.003 0.025 3321 Dihedral : 14.887 89.035 4633 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.05 % Allowed : 25.14 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2624 helix: 1.63 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.26 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 28 PHE 0.029 0.001 PHE C 53 TYR 0.024 0.001 TYR c 41 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 1681) hydrogen bonds : angle 5.24871 ( 5043) covalent geometry : bond 0.00409 (22427) covalent geometry : angle 0.74716 (29725) ********************** 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 640 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 575 time to evaluate : 3.463 Fit side-chains REVERT: B 12 ASP cc_start: 0.8715 (m-30) cc_final: 0.8333 (t0) REVERT: C 43 MET cc_start: 0.8436 (mmm) cc_final: 0.8152 (mmm) REVERT: C 64 MET cc_start: 0.9029 (mmt) cc_final: 0.8508 (mmm) REVERT: D 9 LYS cc_start: 0.8943 (tttt) cc_final: 0.8620 (ttpp) REVERT: E 23 SER cc_start: 0.8993 (p) cc_final: 0.8768 (p) REVERT: G 21 LYS cc_start: 0.8436 (tttt) cc_final: 0.8147 (tptt) REVERT: G 41 TYR cc_start: 0.8524 (t80) cc_final: 0.7966 (t80) REVERT: G 43 MET cc_start: 0.8014 (mtp) cc_final: 0.7787 (mtp) REVERT: I 41 TYR cc_start: 0.8741 (t80) cc_final: 0.8341 (t80) REVERT: K 41 TYR cc_start: 0.8923 (t80) cc_final: 0.8390 (t80) REVERT: L 41 TYR cc_start: 0.8779 (t80) cc_final: 0.7736 (t80) REVERT: L 42 MET cc_start: 0.8488 (tmm) cc_final: 0.8205 (tmm) REVERT: L 64 MET cc_start: 0.8640 (mmm) cc_final: 0.8283 (mmm) REVERT: M 12 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (t0) REVERT: N 22 GLN cc_start: 0.7802 (mm-40) cc_final: 0.7545 (mm-40) REVERT: N 64 MET cc_start: 0.8668 (mmm) cc_final: 0.8384 (mmm) REVERT: N 65 SER cc_start: 0.9040 (t) cc_final: 0.8681 (p) REVERT: Q 8 MET cc_start: 0.8670 (mmm) cc_final: 0.8371 (mmm) REVERT: R 64 MET cc_start: 0.8930 (mmm) cc_final: 0.8609 (mmm) REVERT: S 42 MET cc_start: 0.8526 (tmm) cc_final: 0.8306 (tmm) REVERT: T 6 ASP cc_start: 0.6193 (p0) cc_final: 0.5950 (p0) REVERT: T 42 MET cc_start: 0.8477 (ttp) cc_final: 0.7985 (tmm) REVERT: V 5 THR cc_start: 0.6591 (p) cc_final: 0.6294 (t) REVERT: V 33 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7733 (tm-30) REVERT: V 43 MET cc_start: 0.8579 (mmm) cc_final: 0.8261 (mmm) REVERT: W 21 LYS cc_start: 0.8643 (tptm) cc_final: 0.8359 (tptp) REVERT: Z 9 LYS cc_start: 0.8523 (tttt) cc_final: 0.8115 (tppt) REVERT: Z 22 GLN cc_start: 0.7856 (pm20) cc_final: 0.7555 (mt0) REVERT: Z 40 MET cc_start: 0.8349 (mmm) cc_final: 0.8022 (mmm) REVERT: Z 64 MET cc_start: 0.9037 (mmt) cc_final: 0.8820 (mmm) REVERT: a 8 MET cc_start: 0.8019 (tpp) cc_final: 0.7644 (tpp) REVERT: d 22 GLN cc_start: 0.7927 (mp10) cc_final: 0.7707 (mp10) REVERT: e 15 VAL cc_start: 0.9294 (t) cc_final: 0.8949 (p) REVERT: e 40 MET cc_start: 0.7723 (tpp) cc_final: 0.7415 (tpp) REVERT: e 65 SER cc_start: 0.9033 (t) cc_final: 0.8774 (p) REVERT: f 9 LYS cc_start: 0.8503 (tttp) cc_final: 0.7833 (tppt) REVERT: f 48 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8111 (ptpt) REVERT: f 58 THR cc_start: 0.8893 (m) cc_final: 0.8599 (p) REVERT: f 59 PHE cc_start: 0.8321 (t80) cc_final: 0.8070 (t80) REVERT: g 8 MET cc_start: 0.6866 (mtm) cc_final: 0.6539 (ptp) REVERT: g 65 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8804 (m) REVERT: h 49 PHE cc_start: 0.8782 (m-10) cc_final: 0.8518 (m-10) REVERT: j 42 MET cc_start: 0.8965 (tmm) cc_final: 0.8066 (tmm) REVERT: j 43 MET cc_start: 0.7573 (mtm) cc_final: 0.7057 (mtm) REVERT: j 55 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8673 (pt) REVERT: l 42 MET cc_start: 0.9011 (tmm) cc_final: 0.8539 (tmm) REVERT: l 50 LEU cc_start: 0.9301 (mt) cc_final: 0.8940 (mt) REVERT: m 64 MET cc_start: 0.8731 (mmt) cc_final: 0.8486 (mmt) REVERT: n 8 MET cc_start: 0.7214 (tpt) cc_final: 0.5818 (ptt) REVERT: n 21 LYS cc_start: 0.8240 (tttt) cc_final: 0.7190 (tptp) REVERT: n 42 MET cc_start: 0.7844 (tmm) cc_final: 0.7469 (tmm) outliers start: 65 outliers final: 57 residues processed: 622 average time/residue: 0.3453 time to fit residues: 346.9237 Evaluate side-chains 621 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 560 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE 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 F residue 34 VAL Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 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 7 LEU Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain O residue 15 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V 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 a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 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 60 ILE Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 48 LYS Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 65 SER Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 55 ILE Chi-restraints excluded: chain j residue 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 57 SER 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 231 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.121164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105155 restraints weight = 30008.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108515 restraints weight = 14402.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110528 restraints weight = 8060.964| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22427 Z= 0.146 Angle : 0.733 15.860 29725 Z= 0.354 Chirality : 0.040 0.251 3403 Planarity : 0.003 0.026 3321 Dihedral : 14.581 88.903 4633 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.49 % Allowed : 25.94 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.17), residues: 2624 helix: 1.78 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.05 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 28 PHE 0.057 0.001 PHE H 19 TYR 0.020 0.001 TYR c 41 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 1681) hydrogen bonds : angle 5.20940 ( 5043) covalent geometry : bond 0.00332 (22427) covalent geometry : angle 0.73320 (29725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7311.23 seconds wall clock time: 128 minutes 32.71 seconds (7712.71 seconds total)