Starting phenix.real_space_refine on Sun Sep 29 07:47:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_22460.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_22460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_22460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_22460.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jsv_22460/09_2024/7jsv_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.53, per 1000 atoms: 0.20 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: 5.67 Conformation dependent library (CDL) restraints added in 2.7 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: 2.12 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: 9.25 Time building geometry restraints manager: 6.51 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 44.500 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- 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= 1.236 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 999 time to evaluate : 2.244 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: 0.3218 time to fit residues: 505.0875 Evaluate side-chains 682 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 682 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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= 0.217 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 *********************** 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 fitting. rotamer outliers: 81 poor density : 738 time to evaluate : 2.186 Fit side-chains REVERT: A 9 LYS cc_start: 0.8729 (tttt) cc_final: 0.8405 (tttm) REVERT: B 9 LYS cc_start: 0.8964 (tttt) cc_final: 0.8621 (ttpp) REVERT: C 9 LYS cc_start: 0.8426 (tttt) cc_final: 0.8100 (ttpp) REVERT: D 9 LYS cc_start: 0.8712 (tttt) cc_final: 0.8366 (ttpp) REVERT: D 12 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8520 (t0) REVERT: G 21 LYS cc_start: 0.8240 (tttt) cc_final: 0.7469 (tptt) REVERT: G 41 TYR cc_start: 0.8466 (t80) cc_final: 0.7939 (t80) REVERT: G 51 PHE cc_start: 0.9049 (m-80) cc_final: 0.8798 (m-80) REVERT: G 64 MET cc_start: 0.8910 (mmt) cc_final: 0.8572 (mmm) REVERT: H 8 MET cc_start: 0.7519 (tpp) cc_final: 0.7291 (tpp) REVERT: H 41 TYR cc_start: 0.8679 (t80) cc_final: 0.8076 (t80) REVERT: I 41 TYR cc_start: 0.8616 (t80) cc_final: 0.8255 (t80) REVERT: J 23 SER cc_start: 0.7662 (p) cc_final: 0.7368 (p) REVERT: K 9 LYS cc_start: 0.8279 (tttt) cc_final: 0.7952 (tptt) REVERT: K 69 TYR cc_start: 0.6845 (m-80) cc_final: 0.6410 (m-80) REVERT: L 65 SER cc_start: 0.9388 (t) cc_final: 0.9037 (p) REVERT: N 65 SER cc_start: 0.9079 (t) cc_final: 0.8553 (p) REVERT: P 22 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7449 (mm-40) REVERT: P 33 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8543 (tm-30) REVERT: P 41 TYR cc_start: 0.9119 (t80) cc_final: 0.8867 (t80) REVERT: P 62 ILE cc_start: 0.8793 (mm) cc_final: 0.8579 (mm) REVERT: P 65 SER cc_start: 0.8850 (t) cc_final: 0.8374 (p) REVERT: Q 41 TYR cc_start: 0.8999 (t80) cc_final: 0.8576 (t80) REVERT: R 8 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6965 (tpp) REVERT: R 64 MET cc_start: 0.8742 (mmm) cc_final: 0.8297 (mmm) REVERT: S 21 LYS cc_start: 0.8150 (tptm) cc_final: 0.7695 (tptm) REVERT: T 40 MET cc_start: 0.9040 (mmm) cc_final: 0.8798 (mmm) REVERT: U 41 TYR cc_start: 0.8542 (t80) cc_final: 0.8208 (t80) REVERT: U 64 MET cc_start: 0.8261 (mmt) cc_final: 0.7876 (mmm) REVERT: U 65 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8466 (p) REVERT: X 8 MET cc_start: 0.7567 (tpp) cc_final: 0.7183 (tpp) REVERT: Y 64 MET cc_start: 0.8502 (mmt) cc_final: 0.8219 (mmm) REVERT: Z 41 TYR cc_start: 0.9049 (t80) cc_final: 0.8664 (t80) REVERT: a 10 SER cc_start: 0.9154 (p) cc_final: 0.8878 (t) REVERT: c 42 MET cc_start: 0.8618 (tmm) cc_final: 0.8066 (tmm) REVERT: e 7 LEU cc_start: 0.8819 (tt) cc_final: 0.8426 (tt) REVERT: e 40 MET cc_start: 0.7486 (tpp) cc_final: 0.7215 (tpp) REVERT: e 65 SER cc_start: 0.8886 (t) cc_final: 0.8411 (p) REVERT: g 42 MET cc_start: 0.8602 (tmm) cc_final: 0.7189 (tpt) REVERT: h 6 ASP cc_start: 0.4707 (p0) cc_final: 0.3874 (m-30) REVERT: h 41 TYR cc_start: 0.8635 (t80) cc_final: 0.8414 (t80) REVERT: h 49 PHE cc_start: 0.8815 (m-80) cc_final: 0.8361 (m-80) REVERT: i 9 LYS cc_start: 0.8325 (tttt) cc_final: 0.7949 (tptt) REVERT: j 39 ILE cc_start: 0.9578 (tp) cc_final: 0.9257 (tp) REVERT: j 42 MET cc_start: 0.8956 (tmm) cc_final: 0.8477 (tmm) REVERT: l 42 MET cc_start: 0.9156 (tmm) cc_final: 0.8701 (tmm) REVERT: m 41 TYR cc_start: 0.8504 (t80) cc_final: 0.8246 (t80) REVERT: m 64 MET cc_start: 0.8328 (mmt) cc_final: 0.8001 (mmt) REVERT: n 40 MET cc_start: 0.8217 (mmp) cc_final: 0.7818 (mmt) REVERT: n 65 SER cc_start: 0.8377 (OUTLIER) cc_final: 0.8169 (p) REVERT: o 9 LYS cc_start: 0.8373 (tttt) cc_final: 0.7967 (ttpt) outliers start: 81 outliers final: 39 residues processed: 771 average time/residue: 0.3056 time to fit residues: 383.7145 Evaluate side-chains 670 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 627 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain D residue 12 ASP 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 124 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22427 Z= 0.205 Angle : 0.609 9.749 29725 Z= 0.315 Chirality : 0.041 0.217 3403 Planarity : 0.003 0.017 3321 Dihedral : 15.033 89.836 4633 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 4.64 % Allowed : 18.25 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 2.46 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 28 PHE 0.019 0.001 PHE j 53 TYR 0.014 0.001 TYR T 41 *********************** 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 767 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 668 time to evaluate : 2.202 Fit side-chains REVERT: A 33 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 9 LYS cc_start: 0.8874 (tttt) cc_final: 0.8539 (ttpp) REVERT: C 64 MET cc_start: 0.9237 (tpp) cc_final: 0.8974 (mmt) REVERT: D 9 LYS cc_start: 0.8745 (tttt) cc_final: 0.8481 (ttpp) REVERT: D 12 ASP cc_start: 0.8982 (m-30) cc_final: 0.8769 (t0) REVERT: G 21 LYS cc_start: 0.8282 (tttt) cc_final: 0.7619 (tptt) REVERT: G 23 SER cc_start: 0.8725 (p) cc_final: 0.8460 (p) REVERT: G 41 TYR cc_start: 0.8420 (t80) cc_final: 0.8100 (t80) REVERT: G 64 MET cc_start: 0.8932 (mmt) cc_final: 0.8646 (mmm) REVERT: H 41 TYR cc_start: 0.8660 (t80) cc_final: 0.8198 (t80) REVERT: H 42 MET cc_start: 0.9278 (tmm) cc_final: 0.8876 (tmm) REVERT: J 40 MET cc_start: 0.9146 (mmm) cc_final: 0.8942 (mmm) REVERT: K 9 LYS cc_start: 0.8512 (tttt) cc_final: 0.8263 (tptt) REVERT: L 65 SER cc_start: 0.9272 (t) cc_final: 0.9015 (p) REVERT: N 62 ILE cc_start: 0.8729 (mm) cc_final: 0.8496 (mt) REVERT: N 65 SER cc_start: 0.9068 (t) cc_final: 0.8697 (p) REVERT: O 42 MET cc_start: 0.8935 (tmm) cc_final: 0.8067 (tmm) REVERT: O 43 MET cc_start: 0.8291 (mtm) cc_final: 0.7806 (mtp) REVERT: R 5 THR cc_start: 0.7052 (p) cc_final: 0.6611 (t) REVERT: R 8 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6725 (tpp) REVERT: R 64 MET cc_start: 0.8828 (mmm) cc_final: 0.8481 (mmm) REVERT: S 12 ASP cc_start: 0.8443 (m-30) cc_final: 0.8135 (t0) REVERT: S 21 LYS cc_start: 0.8366 (tptm) cc_final: 0.8136 (tptm) REVERT: T 40 MET cc_start: 0.8879 (mmm) cc_final: 0.8657 (mmm) REVERT: T 42 MET cc_start: 0.8559 (ttp) cc_final: 0.8133 (tmm) REVERT: U 9 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7645 (ttpt) REVERT: U 65 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8670 (p) REVERT: X 40 MET cc_start: 0.8480 (mmm) cc_final: 0.8245 (mmm) REVERT: X 46 ASN cc_start: 0.8732 (t0) cc_final: 0.8239 (t0) REVERT: Y 64 MET cc_start: 0.8566 (mmt) cc_final: 0.8189 (mmm) REVERT: Z 41 TYR cc_start: 0.8993 (t80) cc_final: 0.8510 (t80) REVERT: a 8 MET cc_start: 0.7556 (tpp) cc_final: 0.7233 (tpp) REVERT: a 41 TYR cc_start: 0.8898 (t80) cc_final: 0.8656 (t80) REVERT: c 9 LYS cc_start: 0.8538 (tttt) cc_final: 0.8305 (ttmt) REVERT: e 41 TYR cc_start: 0.8735 (t80) cc_final: 0.8182 (t80) REVERT: e 48 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8602 (ttpp) REVERT: e 65 SER cc_start: 0.9164 (t) cc_final: 0.8709 (p) REVERT: f 59 PHE cc_start: 0.8466 (t80) cc_final: 0.8087 (t80) REVERT: g 42 MET cc_start: 0.8440 (tmm) cc_final: 0.7143 (tpt) REVERT: h 15 VAL cc_start: 0.8870 (m) cc_final: 0.8474 (p) REVERT: h 42 MET cc_start: 0.8500 (tmm) cc_final: 0.7805 (tmm) REVERT: h 48 LYS cc_start: 0.8431 (ptmm) cc_final: 0.7896 (ptpp) REVERT: h 49 PHE cc_start: 0.8751 (m-80) cc_final: 0.8442 (m-80) REVERT: i 8 MET cc_start: 0.7229 (tpp) cc_final: 0.6995 (tpp) REVERT: i 9 LYS cc_start: 0.8627 (tttt) cc_final: 0.8211 (tptt) REVERT: j 39 ILE cc_start: 0.9574 (tp) cc_final: 0.9279 (tp) REVERT: j 42 MET cc_start: 0.8888 (tmm) cc_final: 0.8383 (tmm) REVERT: k 9 LYS cc_start: 0.8444 (tttt) cc_final: 0.8192 (ttpt) REVERT: k 33 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7154 (tm-30) REVERT: l 50 LEU cc_start: 0.9234 (mt) cc_final: 0.8903 (mt) REVERT: m 9 LYS cc_start: 0.7988 (tttt) cc_final: 0.7706 (ptpt) REVERT: m 64 MET cc_start: 0.8635 (mmt) cc_final: 0.8281 (mmt) REVERT: n 40 MET cc_start: 0.8167 (mmp) cc_final: 0.7905 (mmt) REVERT: o 9 LYS cc_start: 0.8602 (tttt) cc_final: 0.8188 (ttmt) outliers start: 99 outliers final: 69 residues processed: 723 average time/residue: 0.3010 time to fit residues: 350.3325 Evaluate side-chains 675 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 604 time to evaluate : 2.214 ------------------------------------------------------------------------------- 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 D residue 56 ILE Chi-restraints excluded: chain E residue 23 SER 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 60 ILE 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 N residue 34 VAL Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 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 S residue 60 ILE Chi-restraints excluded: chain T residue 8 MET 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 U residue 65 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 34 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 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 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain h residue 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 j residue 34 VAL Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 224 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22427 Z= 0.302 Angle : 0.671 9.336 29725 Z= 0.345 Chirality : 0.043 0.220 3403 Planarity : 0.003 0.016 3321 Dihedral : 15.086 89.028 4633 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 5.82 % Allowed : 19.75 % Favored : 74.44 % 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: 2.17 (0.16), residues: 2624 helix: 1.46 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 1.81 (0.34), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 28 PHE 0.020 0.002 PHE j 53 TYR 0.014 0.002 TYR i 41 *********************** 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 767 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 643 time to evaluate : 2.329 Fit side-chains revert: symmetry clash REVERT: B 12 ASP cc_start: 0.8648 (m-30) cc_final: 0.8297 (t0) REVERT: B 64 MET cc_start: 0.9068 (mmm) cc_final: 0.8859 (mmm) REVERT: C 64 MET cc_start: 0.9230 (tpp) cc_final: 0.8837 (mmt) REVERT: D 9 LYS cc_start: 0.8815 (tttt) cc_final: 0.8538 (ttpp) REVERT: D 12 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8626 (t0) REVERT: E 23 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8651 (p) REVERT: F 12 ASP cc_start: 0.9149 (t0) cc_final: 0.8938 (t0) REVERT: G 21 LYS cc_start: 0.8446 (tttt) cc_final: 0.8003 (tptt) REVERT: G 23 SER cc_start: 0.8908 (p) cc_final: 0.8605 (p) REVERT: G 41 TYR cc_start: 0.8505 (t80) cc_final: 0.8157 (t80) REVERT: H 41 TYR cc_start: 0.8941 (t80) cc_final: 0.8475 (t80) REVERT: I 41 TYR cc_start: 0.8744 (t80) cc_final: 0.8465 (t80) REVERT: I 42 MET cc_start: 0.9259 (tmm) cc_final: 0.8829 (tmm) REVERT: K 9 LYS cc_start: 0.8694 (tttt) cc_final: 0.8448 (tptt) REVERT: K 21 LYS cc_start: 0.8536 (tttt) cc_final: 0.8206 (tptp) REVERT: L 41 TYR cc_start: 0.8883 (t80) cc_final: 0.8320 (t80) REVERT: L 65 SER cc_start: 0.9208 (t) cc_final: 0.8958 (p) REVERT: M 62 ILE cc_start: 0.8075 (mm) cc_final: 0.7830 (mt) REVERT: N 22 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7646 (mm-40) REVERT: N 33 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8403 (tm-30) REVERT: N 41 TYR cc_start: 0.8959 (t80) cc_final: 0.8735 (t80) REVERT: N 62 ILE cc_start: 0.8851 (mm) cc_final: 0.8632 (mm) REVERT: N 65 SER cc_start: 0.9116 (t) cc_final: 0.8696 (p) REVERT: P 41 TYR cc_start: 0.9063 (t80) cc_final: 0.8716 (t80) REVERT: P 62 ILE cc_start: 0.8756 (mm) cc_final: 0.8311 (mm) REVERT: R 64 MET cc_start: 0.8848 (mmm) cc_final: 0.8360 (mmm) REVERT: T 5 THR cc_start: 0.6388 (p) cc_final: 0.5645 (t) REVERT: U 65 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8817 (p) REVERT: W 56 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7843 (mt) REVERT: W 65 SER cc_start: 0.9235 (t) cc_final: 0.9024 (p) REVERT: X 46 ASN cc_start: 0.8938 (t0) cc_final: 0.8548 (t0) REVERT: Y 64 MET cc_start: 0.8452 (mmt) cc_final: 0.8152 (mmm) REVERT: a 8 MET cc_start: 0.8048 (tpp) cc_final: 0.7782 (tpp) REVERT: b 22 GLN cc_start: 0.7561 (pm20) cc_final: 0.7339 (mt0) REVERT: b 64 MET cc_start: 0.8266 (mmp) cc_final: 0.7826 (mmp) REVERT: e 40 MET cc_start: 0.7937 (tpp) cc_final: 0.7645 (tpp) REVERT: e 65 SER cc_start: 0.9194 (t) cc_final: 0.8720 (p) REVERT: f 9 LYS cc_start: 0.7954 (tttp) cc_final: 0.7663 (tppt) REVERT: f 21 LYS cc_start: 0.7797 (tttt) cc_final: 0.7552 (tptm) REVERT: h 15 VAL cc_start: 0.9037 (m) cc_final: 0.8729 (p) REVERT: h 21 LYS cc_start: 0.8163 (tttt) cc_final: 0.7934 (tptm) REVERT: h 42 MET cc_start: 0.8543 (tmm) cc_final: 0.8169 (tmm) REVERT: i 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8437 (tptt) REVERT: j 42 MET cc_start: 0.8906 (tmm) cc_final: 0.8319 (tmm) REVERT: k 9 LYS cc_start: 0.8987 (tttt) cc_final: 0.8739 (ttpt) REVERT: l 42 MET cc_start: 0.9127 (tmm) cc_final: 0.8603 (tmm) REVERT: l 50 LEU cc_start: 0.9302 (mt) cc_final: 0.9011 (mt) REVERT: n 8 MET cc_start: 0.6573 (tpt) cc_final: 0.5694 (ptt) REVERT: n 40 MET cc_start: 0.8239 (mmp) cc_final: 0.7946 (mmt) REVERT: n 65 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.8164 (p) REVERT: o 9 LYS cc_start: 0.8891 (tttt) cc_final: 0.8368 (ttpp) outliers start: 124 outliers final: 94 residues processed: 726 average time/residue: 0.2929 time to fit residues: 343.0733 Evaluate side-chains 681 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 582 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain 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 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain 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 8 MET Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 34 VAL 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 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 10 SER Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain d residue 60 ILE Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain e residue 61 THR Chi-restraints excluded: chain f residue 7 LEU Chi-restraints excluded: chain f residue 14 THR Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain 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 34 VAL Chi-restraints excluded: chain j residue 65 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain n residue 65 SER 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 198 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22427 Z= 0.290 Angle : 0.653 12.208 29725 Z= 0.333 Chirality : 0.042 0.197 3403 Planarity : 0.003 0.016 3321 Dihedral : 14.906 88.893 4633 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 5.82 % Allowed : 20.83 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.03 (0.16), residues: 2624 helix: 1.48 (0.11), residues: 2091 sheet: None (None), residues: 0 loop : 1.16 (0.30), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 28 PHE 0.020 0.001 PHE X 53 TYR 0.019 0.002 TYR c 41 *********************** 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 731 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 607 time to evaluate : 2.255 Fit side-chains REVERT: B 12 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8368 (t0) REVERT: B 64 MET cc_start: 0.9180 (mmm) cc_final: 0.8965 (mmm) REVERT: C 64 MET cc_start: 0.9332 (tpp) cc_final: 0.9042 (mmt) REVERT: D 9 LYS cc_start: 0.8822 (tttt) cc_final: 0.8480 (ttpp) REVERT: D 12 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8538 (t0) REVERT: E 23 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8714 (p) REVERT: G 21 LYS cc_start: 0.8575 (tttt) cc_final: 0.7997 (tptt) REVERT: G 23 SER cc_start: 0.8849 (p) cc_final: 0.8491 (p) REVERT: G 41 TYR cc_start: 0.8605 (t80) cc_final: 0.8079 (t80) REVERT: I 41 TYR cc_start: 0.8787 (t80) cc_final: 0.8440 (t80) REVERT: K 21 LYS cc_start: 0.8560 (tttt) cc_final: 0.8260 (tptp) REVERT: K 62 ILE cc_start: 0.8137 (mm) cc_final: 0.7918 (mm) REVERT: L 41 TYR cc_start: 0.8904 (t80) cc_final: 0.8132 (t80) REVERT: M 9 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8049 (tptt) REVERT: N 22 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7610 (mm-40) REVERT: N 62 ILE cc_start: 0.8861 (mm) cc_final: 0.8390 (mm) REVERT: N 65 SER cc_start: 0.9074 (t) cc_final: 0.8725 (p) REVERT: P 41 TYR cc_start: 0.9060 (t80) cc_final: 0.8612 (t80) REVERT: R 64 MET cc_start: 0.8864 (mmm) cc_final: 0.8364 (mmm) REVERT: T 42 MET cc_start: 0.8745 (ttp) cc_final: 0.8509 (ttp) REVERT: U 64 MET cc_start: 0.8646 (mmt) cc_final: 0.8291 (mmt) REVERT: U 65 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8821 (p) REVERT: V 12 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7760 (t70) REVERT: X 14 THR cc_start: 0.8969 (p) cc_final: 0.8746 (t) REVERT: X 46 ASN cc_start: 0.8893 (t0) cc_final: 0.8485 (t0) REVERT: Y 64 MET cc_start: 0.8356 (mmt) cc_final: 0.8009 (mmm) REVERT: a 8 MET cc_start: 0.8050 (tpp) cc_final: 0.7649 (tpp) REVERT: b 64 MET cc_start: 0.8241 (mmp) cc_final: 0.7759 (mmp) REVERT: c 8 MET cc_start: 0.8224 (tpp) cc_final: 0.7570 (tpp) REVERT: c 33 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7256 (tm-30) REVERT: e 40 MET cc_start: 0.7876 (tpp) cc_final: 0.7596 (tpp) REVERT: e 65 SER cc_start: 0.9159 (t) cc_final: 0.8695 (p) REVERT: f 9 LYS cc_start: 0.8145 (tttp) cc_final: 0.7772 (tppt) REVERT: f 21 LYS cc_start: 0.7890 (tttt) cc_final: 0.7489 (tptt) REVERT: f 58 THR cc_start: 0.8831 (m) cc_final: 0.8595 (p) REVERT: h 15 VAL cc_start: 0.8968 (m) cc_final: 0.8731 (p) REVERT: h 42 MET cc_start: 0.8654 (tmm) cc_final: 0.8330 (tmm) REVERT: i 9 LYS cc_start: 0.8864 (tttt) cc_final: 0.8495 (tptt) REVERT: j 42 MET cc_start: 0.9052 (tmm) cc_final: 0.8340 (tmm) REVERT: k 9 LYS cc_start: 0.8930 (tttt) cc_final: 0.8711 (ttpt) REVERT: l 50 LEU cc_start: 0.9322 (mt) cc_final: 0.9021 (mt) REVERT: m 9 LYS cc_start: 0.8787 (tttt) cc_final: 0.8456 (ttpp) REVERT: n 8 MET cc_start: 0.6566 (tpt) cc_final: 0.5633 (ptt) REVERT: n 40 MET cc_start: 0.8174 (mmp) cc_final: 0.7904 (mmt) REVERT: o 9 LYS cc_start: 0.8852 (tttt) cc_final: 0.8416 (ttpp) outliers start: 124 outliers final: 95 residues processed: 691 average time/residue: 0.3011 time to fit residues: 336.3904 Evaluate side-chains 664 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 564 time to evaluate : 2.394 ------------------------------------------------------------------------------- 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 12 ASP Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain E residue 23 SER 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 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 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 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain 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 U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain V residue 12 ASP Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 34 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 12 ASP Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain b residue 34 VAL Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 10 SER Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 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 15 VAL 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 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 44 THR 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 65 SER Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 26 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 29 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 0.2980 chunk 238 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22427 Z= 0.198 Angle : 0.622 10.672 29725 Z= 0.311 Chirality : 0.040 0.177 3403 Planarity : 0.002 0.014 3321 Dihedral : 14.556 89.005 4633 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 4.41 % Allowed : 22.75 % Favored : 72.84 % 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: 2.17 (0.17), residues: 2624 helix: 1.60 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.97 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 28 PHE 0.016 0.001 PHE W 49 TYR 0.013 0.001 TYR X 41 *********************** 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 709 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 615 time to evaluate : 2.275 Fit side-chains REVERT: B 12 ASP cc_start: 0.8603 (m-30) cc_final: 0.8325 (t0) REVERT: B 64 MET cc_start: 0.9126 (mmm) cc_final: 0.8921 (mmm) REVERT: D 9 LYS cc_start: 0.8764 (tttt) cc_final: 0.8479 (ttpp) REVERT: D 12 ASP cc_start: 0.8805 (m-30) cc_final: 0.8401 (t0) REVERT: E 41 TYR cc_start: 0.8597 (t80) cc_final: 0.8330 (t80) REVERT: G 23 SER cc_start: 0.8850 (p) cc_final: 0.8514 (p) REVERT: G 41 TYR cc_start: 0.8565 (t80) cc_final: 0.8093 (t80) REVERT: H 16 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8498 (ttpt) REVERT: I 41 TYR cc_start: 0.8788 (t80) cc_final: 0.8375 (t80) REVERT: K 21 LYS cc_start: 0.8540 (tttt) cc_final: 0.8230 (tptp) REVERT: K 62 ILE cc_start: 0.8039 (mm) cc_final: 0.7813 (mt) REVERT: L 41 TYR cc_start: 0.8839 (t80) cc_final: 0.8187 (t80) REVERT: L 48 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8512 (pptt) REVERT: M 8 MET cc_start: 0.9046 (mtm) cc_final: 0.8778 (mtm) REVERT: M 9 LYS cc_start: 0.8609 (ttpt) cc_final: 0.7973 (tptt) REVERT: M 12 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (t0) REVERT: N 22 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7387 (mm-40) REVERT: N 65 SER cc_start: 0.9122 (t) cc_final: 0.8777 (p) REVERT: P 41 TYR cc_start: 0.8927 (t80) cc_final: 0.8619 (t80) REVERT: R 64 MET cc_start: 0.8861 (mmm) cc_final: 0.8381 (mmm) REVERT: S 42 MET cc_start: 0.8763 (tmm) cc_final: 0.8311 (tmm) REVERT: T 42 MET cc_start: 0.8694 (ttp) cc_final: 0.8141 (tmm) REVERT: U 64 MET cc_start: 0.8578 (mmt) cc_final: 0.8189 (mmt) REVERT: U 65 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8820 (p) REVERT: X 14 THR cc_start: 0.8999 (p) cc_final: 0.8762 (t) REVERT: X 40 MET cc_start: 0.8874 (mmm) cc_final: 0.8613 (mmm) REVERT: X 46 ASN cc_start: 0.8824 (t0) cc_final: 0.8388 (t0) REVERT: Y 41 TYR cc_start: 0.8906 (t80) cc_final: 0.8692 (t80) REVERT: Z 40 MET cc_start: 0.8346 (mmm) cc_final: 0.7985 (mmm) REVERT: b 64 MET cc_start: 0.7997 (mmp) cc_final: 0.7656 (mmp) REVERT: e 65 SER cc_start: 0.9149 (t) cc_final: 0.8712 (p) REVERT: f 9 LYS cc_start: 0.8059 (tttp) cc_final: 0.7651 (tppt) REVERT: f 21 LYS cc_start: 0.7901 (tttt) cc_final: 0.7399 (tptt) REVERT: f 58 THR cc_start: 0.8843 (m) cc_final: 0.8642 (p) REVERT: g 65 SER cc_start: 0.9123 (OUTLIER) cc_final: 0.8877 (m) REVERT: h 42 MET cc_start: 0.8690 (tmm) cc_final: 0.8411 (tmm) REVERT: i 9 LYS cc_start: 0.8803 (tttt) cc_final: 0.8444 (tptt) REVERT: j 42 MET cc_start: 0.9032 (tmm) cc_final: 0.8242 (tmm) REVERT: k 9 LYS cc_start: 0.9009 (tttt) cc_final: 0.8757 (ttpt) REVERT: l 50 LEU cc_start: 0.9280 (mt) cc_final: 0.8988 (mt) REVERT: m 9 LYS cc_start: 0.8641 (tttt) cc_final: 0.8312 (ttpp) REVERT: n 8 MET cc_start: 0.6419 (tpt) cc_final: 0.5599 (ptt) REVERT: n 42 MET cc_start: 0.8052 (tmm) cc_final: 0.7448 (tmm) outliers start: 94 outliers final: 67 residues processed: 677 average time/residue: 0.2910 time to fit residues: 318.2128 Evaluate side-chains 655 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 584 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P 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 U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 15 VAL 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 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 30 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22427 Z= 0.254 Angle : 0.654 11.114 29725 Z= 0.330 Chirality : 0.041 0.235 3403 Planarity : 0.003 0.019 3321 Dihedral : 14.777 89.980 4633 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 4.32 % Allowed : 23.83 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.57 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.77 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 28 PHE 0.023 0.001 PHE j 49 TYR 0.014 0.001 TYR f 41 *********************** 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 695 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 603 time to evaluate : 2.190 Fit side-chains REVERT: A 9 LYS cc_start: 0.8993 (tttm) cc_final: 0.8791 (tttp) REVERT: B 12 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8382 (t0) REVERT: B 64 MET cc_start: 0.9254 (mmm) cc_final: 0.9033 (mmm) REVERT: D 9 LYS cc_start: 0.8784 (tttt) cc_final: 0.8504 (ttpp) REVERT: D 12 ASP cc_start: 0.8751 (m-30) cc_final: 0.8335 (t0) REVERT: G 23 SER cc_start: 0.8945 (p) cc_final: 0.8623 (p) REVERT: G 41 TYR cc_start: 0.8626 (t80) cc_final: 0.8168 (t80) REVERT: I 41 TYR cc_start: 0.8790 (t80) cc_final: 0.8306 (t80) REVERT: K 21 LYS cc_start: 0.8578 (tttt) cc_final: 0.8287 (tptp) REVERT: K 41 TYR cc_start: 0.9027 (t80) cc_final: 0.8463 (t80) REVERT: L 41 TYR cc_start: 0.8862 (t80) cc_final: 0.7872 (t80) REVERT: M 12 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8846 (t0) REVERT: N 8 MET cc_start: 0.7689 (tpp) cc_final: 0.7344 (tpp) REVERT: N 22 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7490 (mm-40) REVERT: N 65 SER cc_start: 0.9163 (t) cc_final: 0.8839 (p) REVERT: P 41 TYR cc_start: 0.8951 (t80) cc_final: 0.8608 (t80) REVERT: Q 40 MET cc_start: 0.8544 (tpp) cc_final: 0.8071 (mmt) REVERT: R 64 MET cc_start: 0.8877 (mmm) cc_final: 0.8482 (mmm) REVERT: U 64 MET cc_start: 0.8734 (mmt) cc_final: 0.8355 (mmt) REVERT: U 65 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8848 (p) REVERT: X 8 MET cc_start: 0.7270 (mmm) cc_final: 0.6856 (mpp) REVERT: Y 64 MET cc_start: 0.8322 (mmt) cc_final: 0.7973 (mmm) REVERT: a 8 MET cc_start: 0.8021 (tpp) cc_final: 0.7665 (tpp) REVERT: b 64 MET cc_start: 0.8076 (mmp) cc_final: 0.7724 (mmp) REVERT: c 33 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7157 (tm-30) REVERT: d 21 LYS cc_start: 0.8078 (tttt) cc_final: 0.7750 (tptt) REVERT: e 40 MET cc_start: 0.7787 (tpp) cc_final: 0.7434 (tpp) REVERT: e 65 SER cc_start: 0.9168 (t) cc_final: 0.8712 (p) REVERT: f 9 LYS cc_start: 0.8221 (tttp) cc_final: 0.7794 (tppt) REVERT: f 21 LYS cc_start: 0.8014 (tttt) cc_final: 0.7490 (tptt) REVERT: f 58 THR cc_start: 0.8854 (m) cc_final: 0.8653 (p) REVERT: h 42 MET cc_start: 0.8670 (tmm) cc_final: 0.8402 (tmm) REVERT: i 9 LYS cc_start: 0.8806 (tttt) cc_final: 0.8547 (tptt) REVERT: j 42 MET cc_start: 0.8923 (tmm) cc_final: 0.8678 (tmm) REVERT: k 9 LYS cc_start: 0.9048 (tttt) cc_final: 0.8788 (ttpt) REVERT: l 42 MET cc_start: 0.9047 (tmm) cc_final: 0.8522 (tmm) REVERT: l 50 LEU cc_start: 0.9322 (mt) cc_final: 0.9039 (mt) REVERT: m 9 LYS cc_start: 0.8717 (tttt) cc_final: 0.8338 (ttpp) REVERT: n 8 MET cc_start: 0.6579 (tpt) cc_final: 0.5780 (ptt) REVERT: n 21 LYS cc_start: 0.8019 (tttt) cc_final: 0.6916 (tptt) REVERT: n 42 MET cc_start: 0.7960 (tmm) cc_final: 0.7314 (tmm) outliers start: 92 outliers final: 80 residues processed: 669 average time/residue: 0.3015 time to fit residues: 324.2671 Evaluate side-chains 658 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 575 time to evaluate : 3.046 ------------------------------------------------------------------------------- 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 12 ASP Chi-restraints excluded: chain B residue 25 VAL 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 F residue 56 ILE Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 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 34 VAL Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain V residue 30 VAL Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain Z residue 30 VAL Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 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 44 THR Chi-restraints excluded: chain h residue 57 SER Chi-restraints excluded: chain i residue 12 ASP Chi-restraints excluded: chain i residue 34 VAL Chi-restraints excluded: chain i residue 56 ILE Chi-restraints excluded: chain j residue 60 ILE Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 40 MET Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 30 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 23 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 43 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 161 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6602 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= 0.202 Angle : 0.659 12.120 29725 Z= 0.326 Chirality : 0.040 0.261 3403 Planarity : 0.003 0.021 3321 Dihedral : 14.510 89.675 4633 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.75 % Allowed : 24.58 % Favored : 71.67 % 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 (0.17), residues: 2624 helix: 1.67 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.44 (0.33), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 28 PHE 0.018 0.001 PHE j 49 TYR 0.016 0.001 TYR f 41 *********************** 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 683 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 603 time to evaluate : 2.165 Fit side-chains REVERT: B 12 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8347 (t0) REVERT: B 64 MET cc_start: 0.9137 (mmm) cc_final: 0.8665 (mmm) REVERT: C 64 MET cc_start: 0.9370 (tpp) cc_final: 0.8980 (mmt) REVERT: D 9 LYS cc_start: 0.8813 (tttt) cc_final: 0.8569 (ttpp) REVERT: D 12 ASP cc_start: 0.8781 (m-30) cc_final: 0.8393 (t0) REVERT: E 41 TYR cc_start: 0.8586 (t80) cc_final: 0.8380 (t80) REVERT: F 64 MET cc_start: 0.8641 (mmm) cc_final: 0.8216 (mmt) REVERT: G 41 TYR cc_start: 0.8568 (t80) cc_final: 0.8121 (t80) REVERT: H 16 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8439 (ttpt) REVERT: I 41 TYR cc_start: 0.8798 (t80) cc_final: 0.8317 (t80) REVERT: K 21 LYS cc_start: 0.8486 (tttt) cc_final: 0.8201 (tptp) REVERT: K 41 TYR cc_start: 0.9013 (t80) cc_final: 0.8321 (t80) REVERT: L 41 TYR cc_start: 0.8832 (t80) cc_final: 0.8120 (t80) REVERT: L 48 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8559 (pttt) REVERT: M 12 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8839 (t0) REVERT: N 8 MET cc_start: 0.7653 (tpp) cc_final: 0.7249 (tpp) REVERT: N 62 ILE cc_start: 0.8389 (mm) cc_final: 0.8089 (mm) REVERT: N 65 SER cc_start: 0.9070 (t) cc_final: 0.8790 (p) REVERT: O 41 TYR cc_start: 0.9174 (t80) cc_final: 0.8927 (t80) REVERT: Q 40 MET cc_start: 0.8497 (tpp) cc_final: 0.8042 (mmt) REVERT: R 64 MET cc_start: 0.8865 (mmm) cc_final: 0.8506 (mmm) REVERT: U 64 MET cc_start: 0.8551 (mmt) cc_final: 0.8162 (mmt) REVERT: U 65 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8855 (p) REVERT: X 40 MET cc_start: 0.8857 (mmm) cc_final: 0.8639 (mmm) REVERT: Z 40 MET cc_start: 0.8189 (mmm) cc_final: 0.7808 (mmm) REVERT: Z 41 TYR cc_start: 0.9043 (t80) cc_final: 0.8402 (t80) REVERT: a 8 MET cc_start: 0.7884 (tpp) cc_final: 0.7524 (tpp) REVERT: b 64 MET cc_start: 0.7988 (mmp) cc_final: 0.7716 (mmp) REVERT: c 64 MET cc_start: 0.8700 (mmt) cc_final: 0.8212 (mmm) REVERT: d 21 LYS cc_start: 0.8016 (tttt) cc_final: 0.7704 (tptt) REVERT: e 40 MET cc_start: 0.7833 (tpp) cc_final: 0.7278 (tpp) REVERT: e 65 SER cc_start: 0.9117 (t) cc_final: 0.8669 (p) REVERT: f 9 LYS cc_start: 0.8160 (tttp) cc_final: 0.7829 (tppt) REVERT: f 41 TYR cc_start: 0.8996 (t80) cc_final: 0.8553 (t80) REVERT: g 65 SER cc_start: 0.9083 (OUTLIER) cc_final: 0.8824 (m) REVERT: h 42 MET cc_start: 0.8684 (tmm) cc_final: 0.8434 (tmm) REVERT: i 9 LYS cc_start: 0.8701 (tttt) cc_final: 0.8494 (tptt) REVERT: j 42 MET cc_start: 0.8945 (tmm) cc_final: 0.8656 (tmm) REVERT: k 9 LYS cc_start: 0.8942 (tttt) cc_final: 0.8691 (ttpt) REVERT: l 42 MET cc_start: 0.8909 (tmm) cc_final: 0.8537 (tmm) REVERT: l 50 LEU cc_start: 0.9276 (mt) cc_final: 0.8990 (mt) REVERT: m 9 LYS cc_start: 0.8601 (tttt) cc_final: 0.8253 (ttpp) REVERT: n 8 MET cc_start: 0.6500 (tpt) cc_final: 0.5675 (ptt) REVERT: n 21 LYS cc_start: 0.8019 (tttt) cc_final: 0.6843 (tptt) REVERT: n 42 MET cc_start: 0.7885 (tmm) cc_final: 0.7459 (tmm) REVERT: o 9 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7832 (ptmt) outliers start: 80 outliers final: 64 residues processed: 653 average time/residue: 0.3001 time to fit residues: 317.1484 Evaluate side-chains 648 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 579 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 12 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain E residue 26 VAL 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 H residue 56 ILE Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 26 VAL Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 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 34 VAL Chi-restraints excluded: chain U residue 43 MET Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain U residue 65 SER Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 10 SER Chi-restraints excluded: chain e residue 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 k residue 40 MET Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 30 VAL Chi-restraints excluded: chain l residue 47 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 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 215 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22427 Z= 0.206 Angle : 0.692 12.968 29725 Z= 0.338 Chirality : 0.040 0.245 3403 Planarity : 0.003 0.023 3321 Dihedral : 14.482 89.566 4633 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.38 % Allowed : 25.28 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.18 (0.17), residues: 2624 helix: 1.73 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.23 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 28 PHE 0.028 0.001 PHE C 53 TYR 0.016 0.001 TYR a 41 *********************** 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 662 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 590 time to evaluate : 2.414 Fit side-chains REVERT: B 12 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8328 (t0) REVERT: B 64 MET cc_start: 0.9144 (mmm) cc_final: 0.8690 (mmm) REVERT: C 64 MET cc_start: 0.9345 (tpp) cc_final: 0.9028 (mmt) REVERT: D 9 LYS cc_start: 0.8757 (tttt) cc_final: 0.8511 (ttpp) REVERT: D 12 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8368 (t0) REVERT: F 64 MET cc_start: 0.8618 (mmm) cc_final: 0.8177 (mmt) REVERT: G 41 TYR cc_start: 0.8629 (t80) cc_final: 0.8211 (t80) REVERT: H 16 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8495 (ttpt) REVERT: I 41 TYR cc_start: 0.8781 (t80) cc_final: 0.8316 (t80) REVERT: I 64 MET cc_start: 0.8780 (mmt) cc_final: 0.8443 (mmp) REVERT: K 21 LYS cc_start: 0.8486 (tttt) cc_final: 0.8236 (tptp) REVERT: K 41 TYR cc_start: 0.9025 (t80) cc_final: 0.8490 (t80) REVERT: L 41 TYR cc_start: 0.8838 (t80) cc_final: 0.8023 (t80) REVERT: L 48 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8552 (pttt) REVERT: M 12 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8833 (t0) REVERT: N 8 MET cc_start: 0.7641 (tpp) cc_final: 0.7335 (tpp) REVERT: N 62 ILE cc_start: 0.8427 (mm) cc_final: 0.8171 (mm) REVERT: N 65 SER cc_start: 0.9042 (t) cc_final: 0.8769 (p) REVERT: O 41 TYR cc_start: 0.9168 (t80) cc_final: 0.8908 (t80) REVERT: Q 40 MET cc_start: 0.8505 (tpp) cc_final: 0.8075 (mmt) REVERT: R 64 MET cc_start: 0.8852 (mmm) cc_final: 0.8510 (mmm) REVERT: S 42 MET cc_start: 0.8634 (tmm) cc_final: 0.8359 (tmm) REVERT: T 42 MET cc_start: 0.8566 (ttp) cc_final: 0.8262 (tmm) REVERT: U 64 MET cc_start: 0.8639 (mmt) cc_final: 0.8319 (mmt) REVERT: U 65 SER cc_start: 0.9125 (t) cc_final: 0.8873 (p) REVERT: V 33 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7637 (tm-30) REVERT: V 43 MET cc_start: 0.8506 (mmm) cc_final: 0.8218 (mmm) REVERT: Z 22 GLN cc_start: 0.7675 (pm20) cc_final: 0.7334 (mp10) REVERT: Z 26 VAL cc_start: 0.9165 (t) cc_final: 0.8944 (t) REVERT: Z 40 MET cc_start: 0.8213 (mmm) cc_final: 0.7841 (mmm) REVERT: Z 41 TYR cc_start: 0.9042 (t80) cc_final: 0.8456 (t80) REVERT: a 8 MET cc_start: 0.7845 (tpp) cc_final: 0.7475 (tpp) REVERT: b 64 MET cc_start: 0.8031 (mmp) cc_final: 0.7706 (mmp) REVERT: d 21 LYS cc_start: 0.7881 (tttt) cc_final: 0.7609 (tptt) REVERT: e 40 MET cc_start: 0.7774 (tpp) cc_final: 0.7383 (tpp) REVERT: e 43 MET cc_start: 0.8509 (ttm) cc_final: 0.8072 (mtp) REVERT: e 65 SER cc_start: 0.9122 (t) cc_final: 0.8687 (p) REVERT: f 9 LYS cc_start: 0.8225 (tttp) cc_final: 0.7839 (tppt) REVERT: f 41 TYR cc_start: 0.9013 (t80) cc_final: 0.8564 (t80) REVERT: g 65 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8832 (m) REVERT: h 42 MET cc_start: 0.8714 (tmm) cc_final: 0.8433 (tmm) REVERT: j 42 MET cc_start: 0.8936 (tmm) cc_final: 0.7953 (tmm) REVERT: k 9 LYS cc_start: 0.8913 (tttt) cc_final: 0.8677 (ttpt) REVERT: l 42 MET cc_start: 0.8915 (tmm) cc_final: 0.8511 (tmm) REVERT: l 50 LEU cc_start: 0.9258 (mt) cc_final: 0.8960 (mt) REVERT: m 9 LYS cc_start: 0.8569 (tttt) cc_final: 0.8224 (ttpp) REVERT: n 8 MET cc_start: 0.6525 (tpt) cc_final: 0.5779 (ptt) REVERT: n 21 LYS cc_start: 0.7959 (tttt) cc_final: 0.6907 (tptt) REVERT: n 42 MET cc_start: 0.7759 (tmm) cc_final: 0.7333 (tmm) REVERT: o 9 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7820 (ptmt) outliers start: 72 outliers final: 61 residues processed: 640 average time/residue: 0.2990 time to fit residues: 308.1135 Evaluate side-chains 637 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 571 time to evaluate : 2.232 ------------------------------------------------------------------------------- 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 12 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 56 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 48 LYS Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P 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 T residue 34 VAL Chi-restraints excluded: chain U residue 43 MET 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 X residue 65 SER Chi-restraints excluded: chain Y residue 56 ILE Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain c residue 12 ASP Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 SER Chi-restraints excluded: chain e residue 60 ILE Chi-restraints excluded: chain f residue 23 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 10 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain 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 k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 162 optimal weight: 30.0000 chunk 245 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 0.9980 chunk 155 optimal weight: 0.0470 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22427 Z= 0.199 Angle : 0.711 13.591 29725 Z= 0.344 Chirality : 0.040 0.244 3403 Planarity : 0.002 0.023 3321 Dihedral : 14.364 89.745 4633 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.91 % Allowed : 26.27 % Favored : 70.83 % 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: 2.23 (0.17), residues: 2624 helix: 1.81 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : 0.01 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 28 PHE 0.016 0.001 PHE H 19 TYR 0.018 0.001 TYR c 41 ********************** 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 656 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 594 time to evaluate : 2.211 Fit side-chains REVERT: B 12 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8237 (t0) REVERT: B 64 MET cc_start: 0.9094 (mmm) cc_final: 0.8699 (mmm) REVERT: C 22 GLN cc_start: 0.8359 (pm20) cc_final: 0.8148 (pm20) REVERT: C 33 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 43 MET cc_start: 0.8369 (mmm) cc_final: 0.8085 (mmt) REVERT: D 9 LYS cc_start: 0.8797 (tttt) cc_final: 0.8560 (ttpp) REVERT: D 12 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8322 (t0) REVERT: F 64 MET cc_start: 0.8588 (mmm) cc_final: 0.8149 (mmt) REVERT: G 41 TYR cc_start: 0.8552 (t80) cc_final: 0.8284 (t80) REVERT: H 16 LYS cc_start: 0.8800 (ttpp) cc_final: 0.8521 (ttpt) REVERT: I 41 TYR cc_start: 0.8754 (t80) cc_final: 0.8345 (t80) REVERT: I 64 MET cc_start: 0.8716 (mmt) cc_final: 0.8348 (mmp) REVERT: K 21 LYS cc_start: 0.8438 (tttt) cc_final: 0.8203 (tptp) REVERT: K 41 TYR cc_start: 0.9012 (t80) cc_final: 0.8337 (t80) REVERT: K 64 MET cc_start: 0.8538 (tpp) cc_final: 0.8160 (mmt) REVERT: L 41 TYR cc_start: 0.8803 (t80) cc_final: 0.8046 (t80) REVERT: M 12 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8808 (t0) REVERT: N 8 MET cc_start: 0.7578 (tpp) cc_final: 0.7255 (tpp) REVERT: N 62 ILE cc_start: 0.8468 (mm) cc_final: 0.8190 (mm) REVERT: N 65 SER cc_start: 0.9038 (t) cc_final: 0.8764 (p) REVERT: O 41 TYR cc_start: 0.9156 (t80) cc_final: 0.8926 (t80) REVERT: Q 40 MET cc_start: 0.8483 (tpp) cc_final: 0.8064 (mmt) REVERT: R 64 MET cc_start: 0.8831 (mmm) cc_final: 0.8504 (mmm) REVERT: S 21 LYS cc_start: 0.8549 (tptm) cc_final: 0.8173 (tptp) REVERT: S 42 MET cc_start: 0.8617 (tmm) cc_final: 0.8383 (tmm) REVERT: T 42 MET cc_start: 0.8490 (ttp) cc_final: 0.8191 (tmm) REVERT: U 64 MET cc_start: 0.8569 (mmt) cc_final: 0.8274 (mmt) REVERT: U 65 SER cc_start: 0.9072 (t) cc_final: 0.8843 (p) REVERT: V 33 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7755 (tm-30) REVERT: V 43 MET cc_start: 0.8434 (mmm) cc_final: 0.8142 (mmm) REVERT: Z 22 GLN cc_start: 0.7421 (pm20) cc_final: 0.7083 (mp10) REVERT: Z 26 VAL cc_start: 0.9130 (t) cc_final: 0.8887 (t) REVERT: Z 40 MET cc_start: 0.8239 (mmm) cc_final: 0.7922 (mmm) REVERT: Z 41 TYR cc_start: 0.9017 (t80) cc_final: 0.8561 (t80) REVERT: a 8 MET cc_start: 0.7761 (tpp) cc_final: 0.7374 (tpp) REVERT: b 64 MET cc_start: 0.8017 (mmp) cc_final: 0.7775 (mmp) REVERT: c 64 MET cc_start: 0.8681 (mmt) cc_final: 0.8191 (mmm) REVERT: e 40 MET cc_start: 0.7827 (tpp) cc_final: 0.7379 (tpp) REVERT: e 65 SER cc_start: 0.9133 (t) cc_final: 0.8703 (p) REVERT: f 9 LYS cc_start: 0.8196 (tttp) cc_final: 0.7808 (tppt) REVERT: f 41 TYR cc_start: 0.8997 (t80) cc_final: 0.8574 (t80) REVERT: g 65 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8807 (m) REVERT: h 42 MET cc_start: 0.8678 (tmm) cc_final: 0.8407 (tmm) REVERT: k 9 LYS cc_start: 0.8864 (tttt) cc_final: 0.8633 (ttpt) REVERT: l 42 MET cc_start: 0.8866 (tmm) cc_final: 0.8517 (tmm) REVERT: l 50 LEU cc_start: 0.9243 (mt) cc_final: 0.8950 (mt) REVERT: m 9 LYS cc_start: 0.8499 (tttt) cc_final: 0.8163 (ttpp) REVERT: n 8 MET cc_start: 0.6510 (tpt) cc_final: 0.5746 (ptt) REVERT: n 21 LYS cc_start: 0.7968 (tttt) cc_final: 0.6916 (tptt) REVERT: n 42 MET cc_start: 0.7671 (tmm) cc_final: 0.7254 (tmm) outliers start: 62 outliers final: 49 residues processed: 637 average time/residue: 0.3039 time to fit residues: 310.7205 Evaluate side-chains 627 residues out of total 2132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 574 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 43 MET Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain P residue 56 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 56 ILE Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 56 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 65 SER Chi-restraints excluded: chain Y residue 43 MET Chi-restraints excluded: chain a residue 9 LYS Chi-restraints excluded: chain a residue 56 ILE Chi-restraints excluded: chain c residue 7 LEU Chi-restraints excluded: chain d residue 29 VAL Chi-restraints excluded: chain d residue 30 VAL Chi-restraints excluded: chain d residue 57 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 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 k residue 7 LEU Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain m residue 56 ILE Chi-restraints excluded: chain m residue 60 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.103035 restraints weight = 30036.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.106320 restraints weight = 14455.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.108341 restraints weight = 8138.624| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22427 Z= 0.235 Angle : 0.723 12.920 29725 Z= 0.353 Chirality : 0.041 0.248 3403 Planarity : 0.003 0.030 3321 Dihedral : 14.503 88.646 4633 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.77 % Allowed : 26.45 % Favored : 70.78 % 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: 2.20 (0.17), residues: 2624 helix: 1.79 (0.11), residues: 2173 sheet: None (None), residues: 0 loop : -0.02 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 28 PHE 0.026 0.001 PHE C 53 TYR 0.019 0.001 TYR a 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5521.71 seconds wall clock time: 99 minutes 22.80 seconds (5962.80 seconds total)