Starting phenix.real_space_refine on Thu Mar 5 16:14:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727.map" model { file = "/net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pzd_13727/03_2026/7pzd_13727_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13338 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8712 2.51 5 N 2358 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13644 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 758 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Restraints were copied for chains: H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 1.43, per 1000 atoms: 0.10 Number of scatterers: 13644 At special positions: 0 Unit cell: (96.03, 99.231, 110.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2466 8.00 N 2358 7.00 C 8712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 514.6 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS G 23 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 Processing helix chain 'G' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLU G 65 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS G 66 " --> pdb=" O ASN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS H 23 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP H 31 " --> pdb=" O MET H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 49 Processing helix chain 'H' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP H 60 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU H 64 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N GLU H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS H 66 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 Processing helix chain 'I' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP I 31 " --> pdb=" O MET I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 Processing helix chain 'I' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 60 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU I 65 " --> pdb=" O PHE I 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 90 Processing helix chain 'J' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP J 31 " --> pdb=" O MET J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 49 Processing helix chain 'J' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE J 59 " --> pdb=" O ALA J 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP J 60 " --> pdb=" O THR J 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS J 66 " --> pdb=" O ASN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS K 23 " --> pdb=" O ASP K 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP K 31 " --> pdb=" O MET K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 49 Processing helix chain 'K' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP K 60 " --> pdb=" O THR K 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS K 66 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'L' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS L 23 " --> pdb=" O ASP L 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP L 31 " --> pdb=" O MET L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 49 Processing helix chain 'L' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP L 60 " --> pdb=" O THR L 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 9.873A pdb=" N GLU L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS L 66 " --> pdb=" O ASN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS M 9 " --> pdb=" O SER M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 31 removed outlier: 3.546A pdb=" N LYS M 23 " --> pdb=" O ASP M 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 49 Processing helix chain 'M' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP M 60 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS M 66 " --> pdb=" O ASN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS N 9 " --> pdb=" O SER N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS N 23 " --> pdb=" O ASP N 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP N 31 " --> pdb=" O MET N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 49 Processing helix chain 'N' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP N 60 " --> pdb=" O THR N 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS N 66 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS O 23 " --> pdb=" O ASP O 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP O 31 " --> pdb=" O MET O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 49 Processing helix chain 'O' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU O 65 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS O 66 " --> pdb=" O ASN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'P' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS P 9 " --> pdb=" O SER P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS P 23 " --> pdb=" O ASP P 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP P 31 " --> pdb=" O MET P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 49 Processing helix chain 'P' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP P 60 " --> pdb=" O THR P 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU P 64 " --> pdb=" O ASP P 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU P 65 " --> pdb=" O PHE P 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS P 66 " --> pdb=" O ASN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 Processing helix chain 'Q' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS Q 9 " --> pdb=" O SER Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS Q 23 " --> pdb=" O ASP Q 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP Q 31 " --> pdb=" O MET Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 49 Processing helix chain 'Q' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP Q 60 " --> pdb=" O THR Q 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS R 9 " --> pdb=" O SER R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS R 23 " --> pdb=" O ASP R 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP R 31 " --> pdb=" O MET R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 49 Processing helix chain 'R' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP R 60 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU R 64 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU R 65 " --> pdb=" O PHE R 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 90 Processing helix chain 'S' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS S 9 " --> pdb=" O SER S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS S 23 " --> pdb=" O ASP S 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP S 31 " --> pdb=" O MET S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 49 Processing helix chain 'S' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP S 60 " --> pdb=" O THR S 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU S 64 " --> pdb=" O ASP S 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU S 65 " --> pdb=" O PHE S 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS S 66 " --> pdb=" O ASN S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 Processing helix chain 'T' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 31 removed outlier: 3.546A pdb=" N LYS T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP T 31 " --> pdb=" O MET T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 49 Processing helix chain 'T' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE T 59 " --> pdb=" O ALA T 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP T 60 " --> pdb=" O THR T 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU T 64 " --> pdb=" O ASP T 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU T 65 " --> pdb=" O PHE T 61 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS T 66 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 90 Processing helix chain 'U' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS U 9 " --> pdb=" O SER U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS U 23 " --> pdb=" O ASP U 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 49 Processing helix chain 'U' and resid 54 through 78 removed outlier: 3.593A pdb=" N ILE U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP U 60 " --> pdb=" O THR U 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU U 65 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 90 Processing helix chain 'V' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS V 9 " --> pdb=" O SER V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 31 removed outlier: 3.544A pdb=" N LYS V 23 " --> pdb=" O ASP V 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP V 31 " --> pdb=" O MET V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP V 60 " --> pdb=" O THR V 56 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 90 Processing helix chain 'W' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS W 23 " --> pdb=" O ASP W 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP W 31 " --> pdb=" O MET W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 49 Processing helix chain 'W' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP W 60 " --> pdb=" O THR W 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU W 65 " --> pdb=" O PHE W 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 90 Processing helix chain 'X' and resid 5 through 16 removed outlier: 3.576A pdb=" N LYS X 9 " --> pdb=" O SER X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 removed outlier: 3.545A pdb=" N LYS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP X 31 " --> pdb=" O MET X 27 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 54 through 78 removed outlier: 3.592A pdb=" N ILE X 59 " --> pdb=" O ALA X 55 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP X 60 " --> pdb=" O THR X 56 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU X 64 " --> pdb=" O ASP X 60 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N GLU X 65 " --> pdb=" O PHE X 61 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 90 756 hydrogen bonds defined for protein. 2268 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: 1.83 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4396 1.34 - 1.46: 2050 1.46 - 1.58: 7342 1.58 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 13968 Sorted by residual: bond pdb=" N VAL K 52 " pdb=" CA VAL K 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL W 52 " pdb=" CA VAL W 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL G 52 " pdb=" CA VAL G 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL H 52 " pdb=" CA VAL H 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 bond pdb=" N VAL Q 52 " pdb=" CA VAL Q 52 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.09e-02 8.42e+03 1.11e+01 ... (remaining 13963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 15263 1.44 - 2.88: 2904 2.88 - 4.32: 445 4.32 - 5.77: 162 5.77 - 7.21: 36 Bond angle restraints: 18810 Sorted by residual: angle pdb=" N ASP L 53 " pdb=" CA ASP L 53 " pdb=" C ASP L 53 " ideal model delta sigma weight residual 113.38 106.17 7.21 1.23e+00 6.61e-01 3.43e+01 angle pdb=" N ASP G 53 " pdb=" CA ASP G 53 " pdb=" C ASP G 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.42e+01 angle pdb=" N ASP T 53 " pdb=" CA ASP T 53 " pdb=" C ASP T 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 angle pdb=" N ASP Q 53 " pdb=" CA ASP Q 53 " pdb=" C ASP Q 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 angle pdb=" N ASP V 53 " pdb=" CA ASP V 53 " pdb=" C ASP V 53 " ideal model delta sigma weight residual 113.38 106.19 7.19 1.23e+00 6.61e-01 3.41e+01 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 7254 15.38 - 30.77: 954 30.77 - 46.15: 216 46.15 - 61.54: 144 61.54 - 76.92: 36 Dihedral angle restraints: 8604 sinusoidal: 3708 harmonic: 4896 Sorted by residual: dihedral pdb=" CA PRO S 33 " pdb=" C PRO S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PRO M 33 " pdb=" C PRO M 33 " pdb=" N PRO M 34 " pdb=" CA PRO M 34 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PRO H 33 " pdb=" C PRO H 33 " pdb=" N PRO H 34 " pdb=" CA PRO H 34 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 8601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 954 0.042 - 0.084: 482 0.084 - 0.126: 292 0.126 - 0.167: 162 0.167 - 0.209: 54 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CA ASP N 53 " pdb=" N ASP N 53 " pdb=" C ASP N 53 " pdb=" CB ASP N 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASP R 53 " pdb=" N ASP R 53 " pdb=" C ASP R 53 " pdb=" CB ASP R 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASP V 53 " pdb=" N ASP V 53 " pdb=" C ASP V 53 " pdb=" CB ASP V 53 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1941 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA P 49 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C ALA P 49 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA P 49 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP P 50 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 49 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ALA S 49 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA S 49 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP S 50 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA V 49 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ALA V 49 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA V 49 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP V 50 " -0.013 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5346 2.89 - 3.39: 12700 3.39 - 3.89: 21161 3.89 - 4.40: 24040 4.40 - 4.90: 41222 Nonbonded interactions: 104469 Sorted by model distance: nonbonded pdb=" OD1 ASP G 82 " pdb=" N LEU G 83 " model vdw 2.384 3.120 nonbonded pdb=" OD1 ASP N 82 " pdb=" N LEU N 83 " model vdw 2.384 3.120 nonbonded pdb=" OD1 ASP U 82 " pdb=" N LEU U 83 " model vdw 2.384 3.120 nonbonded pdb=" OD1 ASP P 82 " pdb=" N LEU P 83 " model vdw 2.384 3.120 nonbonded pdb=" OD1 ASP Q 82 " pdb=" N LEU Q 83 " model vdw 2.384 3.120 ... (remaining 104464 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: 0.02 Found NCS groups: ncs_group { reference = 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' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 10.990 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.010 0.037 13968 Z= 0.588 Angle : 1.241 7.207 18810 Z= 0.880 Chirality : 0.075 0.209 1944 Planarity : 0.007 0.032 2412 Dihedral : 16.787 76.919 5400 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.27 % Allowed : 13.92 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.16), residues: 1620 helix: -2.31 (0.11), residues: 1296 sheet: None (None), residues: 0 loop : -2.09 (0.23), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG U 81 TYR 0.008 0.003 TYR W 13 PHE 0.019 0.004 PHE G 75 TRP 0.011 0.002 TRP J 94 HIS 0.005 0.002 HIS G 28 Details of bonding type rmsd covalent geometry : bond 0.00974 (13968) covalent geometry : angle 1.24143 (18810) hydrogen bonds : bond 0.14194 ( 756) hydrogen bonds : angle 7.36609 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 549 time to evaluate : 0.401 Fit side-chains REVERT: G 43 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7561 (mtp-110) REVERT: G 81 ARG cc_start: 0.7615 (mmt180) cc_final: 0.6678 (ptt180) REVERT: H 43 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7616 (mtp-110) REVERT: H 81 ARG cc_start: 0.7386 (mmt180) cc_final: 0.6374 (ptt180) REVERT: I 81 ARG cc_start: 0.7816 (mmt180) cc_final: 0.6818 (ptt180) REVERT: J 62 ASN cc_start: 0.9029 (m-40) cc_final: 0.8570 (m-40) REVERT: J 81 ARG cc_start: 0.7781 (mmt180) cc_final: 0.6978 (mtp180) REVERT: K 62 ASN cc_start: 0.8968 (m-40) cc_final: 0.8664 (m-40) REVERT: K 89 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8356 (mtm110) REVERT: L 62 ASN cc_start: 0.9027 (m-40) cc_final: 0.8601 (m-40) REVERT: L 81 ARG cc_start: 0.8086 (mmt180) cc_final: 0.7412 (mtm180) REVERT: L 90 ASP cc_start: 0.7450 (t0) cc_final: 0.7234 (t0) REVERT: N 90 ASP cc_start: 0.7613 (t0) cc_final: 0.7291 (t0) REVERT: O 43 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: O 90 ASP cc_start: 0.7692 (t0) cc_final: 0.7492 (t0) REVERT: P 31 ASP cc_start: 0.8417 (m-30) cc_final: 0.8166 (m-30) REVERT: P 70 MET cc_start: 0.8179 (mtp) cc_final: 0.7938 (mtp) REVERT: Q 30 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7834 (mt-10) REVERT: Q 62 ASN cc_start: 0.8841 (m-40) cc_final: 0.8470 (m110) REVERT: Q 90 ASP cc_start: 0.7994 (t0) cc_final: 0.7655 (t0) REVERT: R 62 ASN cc_start: 0.8919 (m-40) cc_final: 0.8314 (m-40) REVERT: S 30 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7181 (mt-10) REVERT: S 43 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7179 (mtp180) REVERT: T 30 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7412 (mt-10) REVERT: T 43 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: T 70 MET cc_start: 0.8088 (mtp) cc_final: 0.7757 (mtp) REVERT: U 16 ASP cc_start: 0.8091 (t0) cc_final: 0.7866 (t0) REVERT: U 30 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7419 (mt-10) REVERT: U 43 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: U 62 ASN cc_start: 0.8991 (m-40) cc_final: 0.8578 (m110) REVERT: V 31 ASP cc_start: 0.8198 (m-30) cc_final: 0.7983 (m-30) REVERT: V 62 ASN cc_start: 0.9131 (m-40) cc_final: 0.8925 (m110) REVERT: X 91 GLU cc_start: 0.7788 (tt0) cc_final: 0.7586 (tt0) outliers start: 18 outliers final: 4 residues processed: 567 average time/residue: 0.1583 time to fit residues: 118.6781 Evaluate side-chains 473 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 463 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 43 ARG Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain J residue 43 ARG Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain L residue 43 ARG Chi-restraints excluded: chain N residue 43 ARG Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 43 ARG Chi-restraints excluded: chain T residue 43 ARG Chi-restraints excluded: chain U residue 43 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN H 45 GLN I 62 ASN J 28 HIS J 45 GLN J 51 HIS K 28 HIS K 45 GLN L 28 HIS L 45 GLN M 28 HIS M 45 GLN M 62 ASN N 28 HIS N 62 ASN O 28 HIS O 45 GLN O 62 ASN P 28 HIS P 62 ASN Q 28 HIS R 28 HIS R 45 GLN S 28 HIS S 62 ASN S 79 ASN T 28 HIS T 45 GLN T 62 ASN U 28 HIS U 45 GLN V 28 HIS V 51 HIS W 28 HIS W 51 HIS W 62 ASN X 28 HIS X 62 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127360 restraints weight = 16956.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131761 restraints weight = 9508.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134667 restraints weight = 6142.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136695 restraints weight = 4389.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138146 restraints weight = 3322.674| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13968 Z= 0.147 Angle : 0.627 6.063 18810 Z= 0.343 Chirality : 0.039 0.146 1944 Planarity : 0.005 0.037 2412 Dihedral : 4.931 29.893 1840 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.31 % Allowed : 18.99 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1620 helix: -0.17 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.24 (0.39), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 89 TYR 0.022 0.002 TYR Q 32 PHE 0.013 0.002 PHE J 25 TRP 0.004 0.001 TRP G 73 HIS 0.008 0.003 HIS V 51 Details of bonding type rmsd covalent geometry : bond 0.00360 (13968) covalent geometry : angle 0.62659 (18810) hydrogen bonds : bond 0.04576 ( 756) hydrogen bonds : angle 4.60772 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 468 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7769 (mmt180) cc_final: 0.6899 (ptt180) REVERT: G 90 ASP cc_start: 0.7804 (m-30) cc_final: 0.7404 (t0) REVERT: I 81 ARG cc_start: 0.7582 (mmt180) cc_final: 0.6463 (ptt180) REVERT: I 90 ASP cc_start: 0.7307 (t0) cc_final: 0.7026 (t0) REVERT: J 13 TYR cc_start: 0.8323 (m-10) cc_final: 0.7961 (m-10) REVERT: J 31 ASP cc_start: 0.8254 (m-30) cc_final: 0.7785 (m-30) REVERT: J 62 ASN cc_start: 0.8886 (m-40) cc_final: 0.8364 (m-40) REVERT: J 90 ASP cc_start: 0.7170 (t0) cc_final: 0.6763 (t0) REVERT: K 13 TYR cc_start: 0.8322 (m-10) cc_final: 0.7939 (m-10) REVERT: K 31 ASP cc_start: 0.8334 (m-30) cc_final: 0.8094 (m-30) REVERT: K 62 ASN cc_start: 0.8878 (m-40) cc_final: 0.8530 (m110) REVERT: K 90 ASP cc_start: 0.7301 (t0) cc_final: 0.6847 (t0) REVERT: L 13 TYR cc_start: 0.8302 (m-10) cc_final: 0.8099 (m-10) REVERT: L 56 THR cc_start: 0.8679 (t) cc_final: 0.8401 (m) REVERT: L 62 ASN cc_start: 0.8900 (m-40) cc_final: 0.8432 (m-40) REVERT: L 70 MET cc_start: 0.8212 (mtm) cc_final: 0.7988 (mtm) REVERT: L 81 ARG cc_start: 0.7892 (mmt180) cc_final: 0.6946 (mtm110) REVERT: N 31 ASP cc_start: 0.8383 (m-30) cc_final: 0.8004 (m-30) REVERT: N 90 ASP cc_start: 0.7557 (t0) cc_final: 0.7126 (t0) REVERT: O 51 HIS cc_start: 0.8279 (p-80) cc_final: 0.8073 (p90) REVERT: O 90 ASP cc_start: 0.7784 (t0) cc_final: 0.7322 (t0) REVERT: P 27 MET cc_start: 0.8406 (ttt) cc_final: 0.8033 (ttt) REVERT: P 31 ASP cc_start: 0.8375 (m-30) cc_final: 0.8167 (m-30) REVERT: P 90 ASP cc_start: 0.7629 (t0) cc_final: 0.7190 (t0) REVERT: Q 62 ASN cc_start: 0.8667 (m-40) cc_final: 0.8349 (m110) REVERT: Q 90 ASP cc_start: 0.7799 (t0) cc_final: 0.7318 (t0) REVERT: R 62 ASN cc_start: 0.8620 (m-40) cc_final: 0.7947 (m110) REVERT: R 90 ASP cc_start: 0.7576 (t0) cc_final: 0.7258 (t0) REVERT: T 30 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7447 (mt-10) REVERT: U 31 ASP cc_start: 0.7983 (m-30) cc_final: 0.7768 (m-30) REVERT: U 62 ASN cc_start: 0.8896 (m-40) cc_final: 0.8422 (m110) REVERT: U 70 MET cc_start: 0.7878 (mtp) cc_final: 0.7673 (ttm) REVERT: V 36 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7204 (mtpp) REVERT: V 62 ASN cc_start: 0.8999 (m-40) cc_final: 0.8701 (m-40) REVERT: V 85 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7361 (mt-10) REVERT: W 16 ASP cc_start: 0.8436 (t0) cc_final: 0.7928 (t0) REVERT: W 90 ASP cc_start: 0.7622 (t0) cc_final: 0.7403 (t0) REVERT: X 36 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.7021 (mtpt) outliers start: 47 outliers final: 23 residues processed: 489 average time/residue: 0.1506 time to fit residues: 99.4071 Evaluate side-chains 467 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 442 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 51 HIS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 51 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain L residue 47 GLU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 51 HIS Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 88 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 GLN ** H 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123921 restraints weight = 17072.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128137 restraints weight = 9646.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130975 restraints weight = 6311.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132861 restraints weight = 4532.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134366 restraints weight = 3473.236| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13968 Z= 0.169 Angle : 0.593 5.909 18810 Z= 0.321 Chirality : 0.038 0.156 1944 Planarity : 0.005 0.040 2412 Dihedral : 4.283 15.016 1800 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.95 % Allowed : 20.04 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.21), residues: 1620 helix: 0.32 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.79 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 89 TYR 0.022 0.002 TYR J 84 PHE 0.015 0.002 PHE G 25 TRP 0.003 0.001 TRP U 73 HIS 0.008 0.002 HIS V 51 Details of bonding type rmsd covalent geometry : bond 0.00414 (13968) covalent geometry : angle 0.59256 (18810) hydrogen bonds : bond 0.04825 ( 756) hydrogen bonds : angle 3.98943 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 452 time to evaluate : 0.576 Fit side-chains REVERT: G 81 ARG cc_start: 0.7928 (mmt180) cc_final: 0.6892 (ptt180) REVERT: G 90 ASP cc_start: 0.7868 (m-30) cc_final: 0.7586 (t0) REVERT: H 90 ASP cc_start: 0.7714 (t0) cc_final: 0.7388 (t0) REVERT: I 81 ARG cc_start: 0.7619 (mmt180) cc_final: 0.6419 (ptp-170) REVERT: I 90 ASP cc_start: 0.7656 (t0) cc_final: 0.7309 (t0) REVERT: J 13 TYR cc_start: 0.8347 (m-10) cc_final: 0.7790 (m-10) REVERT: J 31 ASP cc_start: 0.8228 (m-30) cc_final: 0.7820 (m-30) REVERT: J 62 ASN cc_start: 0.8927 (m-40) cc_final: 0.8463 (m-40) REVERT: J 90 ASP cc_start: 0.7197 (t0) cc_final: 0.6670 (t0) REVERT: K 13 TYR cc_start: 0.8379 (m-10) cc_final: 0.7906 (m-10) REVERT: K 16 ASP cc_start: 0.8773 (t0) cc_final: 0.8405 (t0) REVERT: K 62 ASN cc_start: 0.8903 (m-40) cc_final: 0.8486 (m-40) REVERT: K 90 ASP cc_start: 0.7321 (t0) cc_final: 0.6856 (t0) REVERT: L 13 TYR cc_start: 0.8392 (m-10) cc_final: 0.7978 (m-10) REVERT: L 62 ASN cc_start: 0.8886 (m-40) cc_final: 0.8508 (m-40) REVERT: L 81 ARG cc_start: 0.7948 (mmt180) cc_final: 0.6635 (mtm180) REVERT: N 31 ASP cc_start: 0.8258 (m-30) cc_final: 0.7891 (m-30) REVERT: N 90 ASP cc_start: 0.7585 (t0) cc_final: 0.7192 (t0) REVERT: O 15 GLU cc_start: 0.7684 (tt0) cc_final: 0.7448 (tt0) REVERT: O 17 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8596 (mp) REVERT: O 90 ASP cc_start: 0.7807 (t0) cc_final: 0.7354 (t0) REVERT: P 27 MET cc_start: 0.8464 (ttt) cc_final: 0.8144 (ttt) REVERT: P 90 ASP cc_start: 0.7593 (t0) cc_final: 0.7274 (t0) REVERT: Q 62 ASN cc_start: 0.8718 (m-40) cc_final: 0.8412 (m-40) REVERT: Q 90 ASP cc_start: 0.7812 (t0) cc_final: 0.7327 (t0) REVERT: R 62 ASN cc_start: 0.8717 (m-40) cc_final: 0.8051 (m110) REVERT: R 90 ASP cc_start: 0.7390 (t0) cc_final: 0.7090 (t0) REVERT: S 27 MET cc_start: 0.8643 (ttp) cc_final: 0.8410 (ttt) REVERT: U 31 ASP cc_start: 0.8059 (m-30) cc_final: 0.7796 (m-30) REVERT: U 35 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7173 (tm-30) REVERT: U 62 ASN cc_start: 0.9011 (m-40) cc_final: 0.8551 (m110) REVERT: U 90 ASP cc_start: 0.7622 (t0) cc_final: 0.7384 (t0) REVERT: V 32 TYR cc_start: 0.8307 (t80) cc_final: 0.7985 (t80) REVERT: V 36 LYS cc_start: 0.7742 (mttt) cc_final: 0.7343 (mtpp) REVERT: V 62 ASN cc_start: 0.9102 (m-40) cc_final: 0.8759 (m-40) REVERT: V 85 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7346 (mt-10) REVERT: W 16 ASP cc_start: 0.8494 (t70) cc_final: 0.8072 (t0) REVERT: W 36 LYS cc_start: 0.7347 (mtpp) cc_final: 0.7120 (mtpp) REVERT: W 70 MET cc_start: 0.8009 (mtp) cc_final: 0.7774 (mtp) REVERT: X 15 GLU cc_start: 0.7602 (tt0) cc_final: 0.7387 (tt0) REVERT: X 36 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7227 (mtpt) outliers start: 42 outliers final: 28 residues processed: 468 average time/residue: 0.1497 time to fit residues: 93.9862 Evaluate side-chains 459 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 429 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 56 THR Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.0770 chunk 77 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 51 HIS S 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123632 restraints weight = 17049.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127776 restraints weight = 9587.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130711 restraints weight = 6295.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132671 restraints weight = 4478.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134091 restraints weight = 3409.634| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13968 Z= 0.159 Angle : 0.570 5.250 18810 Z= 0.308 Chirality : 0.037 0.155 1944 Planarity : 0.005 0.044 2412 Dihedral : 4.202 15.802 1800 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.52 % Allowed : 21.38 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1620 helix: 0.49 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 89 TYR 0.021 0.002 TYR M 32 PHE 0.013 0.002 PHE H 25 TRP 0.005 0.001 TRP H 68 HIS 0.007 0.002 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00391 (13968) covalent geometry : angle 0.56955 (18810) hydrogen bonds : bond 0.04554 ( 756) hydrogen bonds : angle 3.82049 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 442 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7881 (mmt180) cc_final: 0.6873 (ptp-170) REVERT: G 90 ASP cc_start: 0.7854 (m-30) cc_final: 0.7605 (t0) REVERT: H 90 ASP cc_start: 0.7725 (t0) cc_final: 0.7330 (t0) REVERT: I 81 ARG cc_start: 0.7612 (mmt180) cc_final: 0.6389 (ptp-170) REVERT: I 90 ASP cc_start: 0.7771 (t0) cc_final: 0.7461 (t0) REVERT: J 13 TYR cc_start: 0.8367 (m-10) cc_final: 0.8007 (m-10) REVERT: J 31 ASP cc_start: 0.8210 (m-30) cc_final: 0.7796 (m-30) REVERT: J 62 ASN cc_start: 0.8906 (m-40) cc_final: 0.8442 (m110) REVERT: J 90 ASP cc_start: 0.7293 (t0) cc_final: 0.6879 (t0) REVERT: K 13 TYR cc_start: 0.8439 (m-10) cc_final: 0.7877 (m-10) REVERT: K 62 ASN cc_start: 0.8887 (m-40) cc_final: 0.8463 (m-40) REVERT: K 90 ASP cc_start: 0.7376 (t0) cc_final: 0.6887 (t0) REVERT: L 13 TYR cc_start: 0.8418 (m-10) cc_final: 0.7939 (m-10) REVERT: L 62 ASN cc_start: 0.8862 (m-40) cc_final: 0.8454 (m-40) REVERT: L 81 ARG cc_start: 0.7965 (mmt180) cc_final: 0.6598 (mtm110) REVERT: M 90 ASP cc_start: 0.7388 (t0) cc_final: 0.7170 (t0) REVERT: N 31 ASP cc_start: 0.8249 (m-30) cc_final: 0.7905 (m-30) REVERT: N 90 ASP cc_start: 0.7666 (t0) cc_final: 0.7266 (t0) REVERT: O 17 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8497 (mp) REVERT: O 90 ASP cc_start: 0.7842 (t0) cc_final: 0.7422 (t0) REVERT: P 27 MET cc_start: 0.8426 (ttp) cc_final: 0.8124 (ttt) REVERT: P 90 ASP cc_start: 0.7535 (t0) cc_final: 0.7186 (t0) REVERT: Q 62 ASN cc_start: 0.8718 (m-40) cc_final: 0.8427 (m110) REVERT: Q 90 ASP cc_start: 0.7851 (t0) cc_final: 0.7317 (t0) REVERT: R 62 ASN cc_start: 0.8729 (m-40) cc_final: 0.8113 (m110) REVERT: R 90 ASP cc_start: 0.7432 (t0) cc_final: 0.7093 (t0) REVERT: S 27 MET cc_start: 0.8615 (ttp) cc_final: 0.8369 (ttt) REVERT: S 31 ASP cc_start: 0.7938 (m-30) cc_final: 0.7697 (m-30) REVERT: S 85 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6545 (mt-10) REVERT: U 31 ASP cc_start: 0.8078 (m-30) cc_final: 0.7783 (m-30) REVERT: U 62 ASN cc_start: 0.9011 (m-40) cc_final: 0.8592 (m110) REVERT: V 32 TYR cc_start: 0.8356 (t80) cc_final: 0.8115 (t80) REVERT: V 36 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7324 (mtpp) REVERT: V 62 ASN cc_start: 0.9087 (m-40) cc_final: 0.8745 (m-40) REVERT: W 12 ARG cc_start: 0.7685 (mmm160) cc_final: 0.7385 (tpt90) REVERT: W 16 ASP cc_start: 0.8437 (t70) cc_final: 0.8053 (t0) REVERT: W 36 LYS cc_start: 0.7457 (mtpp) cc_final: 0.7181 (mtpp) REVERT: W 70 MET cc_start: 0.8006 (mtp) cc_final: 0.7728 (mtp) REVERT: W 91 GLU cc_start: 0.7786 (tt0) cc_final: 0.7420 (tt0) REVERT: X 36 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7552 (mtpt) outliers start: 50 outliers final: 29 residues processed: 469 average time/residue: 0.1421 time to fit residues: 90.0615 Evaluate side-chains 464 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 432 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 27 MET Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 56 THR Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 56 THR Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 56 THR Chi-restraints excluded: chain X residue 93 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 150 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109948 restraints weight = 17869.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113769 restraints weight = 10186.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116406 restraints weight = 6654.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118261 restraints weight = 4751.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119711 restraints weight = 3603.951| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.130 Angle : 0.544 5.938 18810 Z= 0.296 Chirality : 0.035 0.141 1944 Planarity : 0.005 0.048 2412 Dihedral : 4.075 15.618 1800 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.38 % Allowed : 21.66 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1620 helix: 0.76 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 89 TYR 0.027 0.002 TYR M 32 PHE 0.016 0.001 PHE I 25 TRP 0.003 0.000 TRP U 68 HIS 0.007 0.002 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00317 (13968) covalent geometry : angle 0.54429 (18810) hydrogen bonds : bond 0.04028 ( 756) hydrogen bonds : angle 3.69505 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 436 time to evaluate : 0.629 Fit side-chains REVERT: G 81 ARG cc_start: 0.7962 (mmt180) cc_final: 0.6835 (mtp180) REVERT: G 90 ASP cc_start: 0.8008 (m-30) cc_final: 0.7670 (t0) REVERT: H 90 ASP cc_start: 0.7798 (t0) cc_final: 0.7313 (t0) REVERT: I 81 ARG cc_start: 0.7668 (mmt180) cc_final: 0.6306 (ptp-170) REVERT: I 90 ASP cc_start: 0.7986 (t0) cc_final: 0.7689 (t0) REVERT: J 13 TYR cc_start: 0.8251 (m-10) cc_final: 0.7857 (m-10) REVERT: J 31 ASP cc_start: 0.8277 (m-30) cc_final: 0.7784 (m-30) REVERT: J 62 ASN cc_start: 0.8831 (m-40) cc_final: 0.8302 (m-40) REVERT: J 90 ASP cc_start: 0.7399 (t0) cc_final: 0.6936 (t0) REVERT: K 13 TYR cc_start: 0.8309 (m-10) cc_final: 0.7907 (m-10) REVERT: K 16 ASP cc_start: 0.8752 (t0) cc_final: 0.8377 (t0) REVERT: K 50 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8336 (t0) REVERT: K 62 ASN cc_start: 0.8888 (m-40) cc_final: 0.8431 (m-40) REVERT: K 90 ASP cc_start: 0.7565 (t0) cc_final: 0.7052 (t0) REVERT: L 13 TYR cc_start: 0.8337 (m-10) cc_final: 0.7918 (m-10) REVERT: L 62 ASN cc_start: 0.8882 (m-40) cc_final: 0.8375 (m110) REVERT: L 81 ARG cc_start: 0.8043 (mmt180) cc_final: 0.6635 (mtm110) REVERT: M 90 ASP cc_start: 0.7649 (t0) cc_final: 0.7412 (t0) REVERT: N 31 ASP cc_start: 0.8297 (m-30) cc_final: 0.7901 (m-30) REVERT: N 90 ASP cc_start: 0.7787 (t0) cc_final: 0.7346 (t0) REVERT: O 90 ASP cc_start: 0.7973 (t0) cc_final: 0.7455 (t0) REVERT: P 90 ASP cc_start: 0.7647 (t0) cc_final: 0.7253 (t0) REVERT: Q 62 ASN cc_start: 0.8721 (m-40) cc_final: 0.8425 (m110) REVERT: Q 90 ASP cc_start: 0.8008 (t0) cc_final: 0.7454 (t0) REVERT: R 62 ASN cc_start: 0.8735 (m-40) cc_final: 0.8090 (m110) REVERT: R 88 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8219 (mtmt) REVERT: R 90 ASP cc_start: 0.7437 (t0) cc_final: 0.7061 (t0) REVERT: S 27 MET cc_start: 0.8598 (ttp) cc_final: 0.8387 (ttt) REVERT: S 31 ASP cc_start: 0.8052 (m-30) cc_final: 0.7846 (m-30) REVERT: S 85 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6718 (mt-10) REVERT: T 47 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6824 (mm-30) REVERT: T 90 ASP cc_start: 0.7977 (t0) cc_final: 0.7756 (t0) REVERT: U 30 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7546 (mt-10) REVERT: U 31 ASP cc_start: 0.8139 (m-30) cc_final: 0.7794 (m-30) REVERT: U 47 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6845 (mm-30) REVERT: U 62 ASN cc_start: 0.8997 (m-40) cc_final: 0.8498 (m110) REVERT: U 90 ASP cc_start: 0.7714 (t0) cc_final: 0.7338 (t0) REVERT: V 32 TYR cc_start: 0.8499 (t80) cc_final: 0.8273 (t80) REVERT: V 36 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7267 (mtpp) REVERT: V 62 ASN cc_start: 0.9022 (m-40) cc_final: 0.8670 (m-40) REVERT: W 12 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7459 (tpt90) REVERT: W 16 ASP cc_start: 0.8417 (t70) cc_final: 0.8046 (t0) REVERT: W 36 LYS cc_start: 0.7455 (mtpp) cc_final: 0.7149 (mtpp) REVERT: W 70 MET cc_start: 0.7969 (mtp) cc_final: 0.7662 (mtp) REVERT: X 15 GLU cc_start: 0.7679 (tt0) cc_final: 0.7388 (tt0) REVERT: X 36 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7478 (mtpt) REVERT: X 90 ASP cc_start: 0.8164 (t0) cc_final: 0.7936 (t0) REVERT: X 91 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7416 (tm-30) outliers start: 48 outliers final: 32 residues processed: 458 average time/residue: 0.1522 time to fit residues: 94.1688 Evaluate side-chains 460 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 425 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 56 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 56 THR Chi-restraints excluded: chain X residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 18 optimal weight: 10.0000 chunk 129 optimal weight: 0.0000 chunk 46 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.127810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109221 restraints weight = 17757.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113049 restraints weight = 10210.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115696 restraints weight = 6672.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117557 restraints weight = 4793.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118873 restraints weight = 3659.913| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.129 Angle : 0.539 5.951 18810 Z= 0.292 Chirality : 0.035 0.142 1944 Planarity : 0.005 0.048 2412 Dihedral : 4.013 15.329 1800 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.16 % Allowed : 23.00 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1620 helix: 0.99 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.94 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 89 TYR 0.021 0.002 TYR M 32 PHE 0.013 0.001 PHE G 25 TRP 0.004 0.000 TRP H 68 HIS 0.007 0.002 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00315 (13968) covalent geometry : angle 0.53918 (18810) hydrogen bonds : bond 0.03996 ( 756) hydrogen bonds : angle 3.65615 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 431 time to evaluate : 0.523 Fit side-chains REVERT: G 81 ARG cc_start: 0.7948 (mmt180) cc_final: 0.6811 (mtp180) REVERT: G 90 ASP cc_start: 0.8159 (m-30) cc_final: 0.7767 (t0) REVERT: H 90 ASP cc_start: 0.7925 (t0) cc_final: 0.7440 (t0) REVERT: I 90 ASP cc_start: 0.8104 (t0) cc_final: 0.7582 (t0) REVERT: J 13 TYR cc_start: 0.8208 (m-10) cc_final: 0.7837 (m-10) REVERT: J 31 ASP cc_start: 0.8253 (m-30) cc_final: 0.7780 (m-30) REVERT: J 62 ASN cc_start: 0.8838 (m-40) cc_final: 0.8419 (m-40) REVERT: J 90 ASP cc_start: 0.7365 (t0) cc_final: 0.6939 (t0) REVERT: K 13 TYR cc_start: 0.8291 (m-10) cc_final: 0.7868 (m-10) REVERT: K 50 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8375 (t0) REVERT: K 62 ASN cc_start: 0.8791 (m-40) cc_final: 0.8435 (m-40) REVERT: K 90 ASP cc_start: 0.7483 (t0) cc_final: 0.7053 (t0) REVERT: L 13 TYR cc_start: 0.8314 (m-10) cc_final: 0.7885 (m-10) REVERT: L 16 ASP cc_start: 0.8721 (t0) cc_final: 0.8331 (t0) REVERT: L 62 ASN cc_start: 0.8898 (m-40) cc_final: 0.8517 (m-40) REVERT: M 90 ASP cc_start: 0.7664 (t0) cc_final: 0.7407 (t0) REVERT: N 31 ASP cc_start: 0.8274 (m-30) cc_final: 0.7864 (m-30) REVERT: N 90 ASP cc_start: 0.7814 (t0) cc_final: 0.7377 (t0) REVERT: O 90 ASP cc_start: 0.7974 (t0) cc_final: 0.7472 (t0) REVERT: P 90 ASP cc_start: 0.7574 (t0) cc_final: 0.7246 (t0) REVERT: Q 62 ASN cc_start: 0.8750 (m-40) cc_final: 0.8434 (m110) REVERT: Q 90 ASP cc_start: 0.8018 (t0) cc_final: 0.7464 (t0) REVERT: R 62 ASN cc_start: 0.8744 (m-40) cc_final: 0.8089 (m110) REVERT: R 90 ASP cc_start: 0.7506 (t0) cc_final: 0.7125 (t0) REVERT: S 31 ASP cc_start: 0.8096 (m-30) cc_final: 0.7874 (m-30) REVERT: S 85 GLU cc_start: 0.7040 (mt-10) cc_final: 0.6716 (mt-10) REVERT: T 90 ASP cc_start: 0.8137 (t0) cc_final: 0.7865 (t0) REVERT: U 31 ASP cc_start: 0.8120 (m-30) cc_final: 0.7752 (m-30) REVERT: U 47 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6864 (mm-30) REVERT: U 62 ASN cc_start: 0.8989 (m-40) cc_final: 0.8478 (m110) REVERT: U 90 ASP cc_start: 0.7787 (t0) cc_final: 0.7564 (t0) REVERT: V 27 MET cc_start: 0.8439 (ttp) cc_final: 0.8181 (ttt) REVERT: V 36 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7222 (mtpp) REVERT: V 62 ASN cc_start: 0.9057 (m-40) cc_final: 0.8690 (m-40) REVERT: W 12 ARG cc_start: 0.7646 (mmm160) cc_final: 0.7374 (tpt90) REVERT: W 16 ASP cc_start: 0.8396 (t70) cc_final: 0.8157 (t0) REVERT: W 36 LYS cc_start: 0.7419 (mtpp) cc_final: 0.7126 (mtpp) REVERT: X 15 GLU cc_start: 0.7651 (tt0) cc_final: 0.7422 (tt0) REVERT: X 36 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7484 (mtpt) REVERT: X 90 ASP cc_start: 0.8253 (t0) cc_final: 0.7982 (t0) REVERT: X 91 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7431 (tm-30) outliers start: 45 outliers final: 29 residues processed: 451 average time/residue: 0.1466 time to fit residues: 89.3169 Evaluate side-chains 457 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 425 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain S residue 15 GLU Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 36 LYS Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102800 restraints weight = 18363.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106397 restraints weight = 10641.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108960 restraints weight = 7114.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110703 restraints weight = 5174.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111982 restraints weight = 4025.976| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13968 Z= 0.236 Angle : 0.630 7.050 18810 Z= 0.343 Chirality : 0.039 0.158 1944 Planarity : 0.006 0.050 2412 Dihedral : 4.376 15.716 1800 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.23 % Allowed : 23.56 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.20), residues: 1620 helix: 0.71 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.07 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 89 TYR 0.027 0.003 TYR M 32 PHE 0.013 0.002 PHE I 25 TRP 0.006 0.001 TRP U 73 HIS 0.008 0.002 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00576 (13968) covalent geometry : angle 0.62967 (18810) hydrogen bonds : bond 0.05375 ( 756) hydrogen bonds : angle 3.86128 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 447 time to evaluate : 0.547 Fit side-chains REVERT: G 81 ARG cc_start: 0.7984 (mmt180) cc_final: 0.6732 (mtp180) REVERT: G 90 ASP cc_start: 0.8022 (m-30) cc_final: 0.7453 (t0) REVERT: H 90 ASP cc_start: 0.8062 (t0) cc_final: 0.7530 (t0) REVERT: I 81 ARG cc_start: 0.7714 (mmt180) cc_final: 0.6252 (ptp-170) REVERT: I 90 ASP cc_start: 0.8218 (t0) cc_final: 0.7697 (t0) REVERT: J 13 TYR cc_start: 0.8288 (m-10) cc_final: 0.7776 (m-10) REVERT: J 31 ASP cc_start: 0.8165 (m-30) cc_final: 0.7738 (m-30) REVERT: J 62 ASN cc_start: 0.8957 (m-40) cc_final: 0.8488 (m110) REVERT: J 70 MET cc_start: 0.8532 (ttp) cc_final: 0.8115 (ttm) REVERT: J 85 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7233 (tm-30) REVERT: K 13 TYR cc_start: 0.8376 (m-10) cc_final: 0.7846 (m-10) REVERT: K 16 ASP cc_start: 0.8739 (t0) cc_final: 0.8451 (t0) REVERT: K 62 ASN cc_start: 0.8931 (m110) cc_final: 0.8537 (m-40) REVERT: K 90 ASP cc_start: 0.7464 (t0) cc_final: 0.7041 (t0) REVERT: L 13 TYR cc_start: 0.8401 (m-10) cc_final: 0.7779 (m-10) REVERT: L 62 ASN cc_start: 0.8941 (m-40) cc_final: 0.8541 (m-40) REVERT: L 81 ARG cc_start: 0.8010 (mmt180) cc_final: 0.6568 (mtm110) REVERT: M 90 ASP cc_start: 0.7754 (t0) cc_final: 0.7484 (t0) REVERT: N 31 ASP cc_start: 0.8314 (m-30) cc_final: 0.7933 (m-30) REVERT: N 90 ASP cc_start: 0.8018 (t0) cc_final: 0.7537 (t0) REVERT: O 17 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8535 (mp) REVERT: O 90 ASP cc_start: 0.8056 (t0) cc_final: 0.7530 (t0) REVERT: P 90 ASP cc_start: 0.7825 (t0) cc_final: 0.7367 (t0) REVERT: Q 62 ASN cc_start: 0.8874 (m-40) cc_final: 0.8536 (m110) REVERT: R 62 ASN cc_start: 0.8931 (m-40) cc_final: 0.8234 (m110) REVERT: R 90 ASP cc_start: 0.7652 (t0) cc_final: 0.7252 (t0) REVERT: S 85 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6640 (mt-10) REVERT: T 90 ASP cc_start: 0.8209 (t0) cc_final: 0.7935 (t0) REVERT: U 35 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7156 (tm-30) REVERT: U 47 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6897 (mm-30) REVERT: U 62 ASN cc_start: 0.9128 (m-40) cc_final: 0.8720 (m110) REVERT: U 90 ASP cc_start: 0.7949 (t0) cc_final: 0.7710 (t0) REVERT: V 36 LYS cc_start: 0.8004 (mttt) cc_final: 0.7520 (mtpt) REVERT: V 62 ASN cc_start: 0.9233 (m-40) cc_final: 0.8933 (m-40) REVERT: W 12 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7520 (tpt90) REVERT: W 16 ASP cc_start: 0.8432 (t70) cc_final: 0.8223 (t0) REVERT: W 90 ASP cc_start: 0.7688 (t0) cc_final: 0.7396 (t0) REVERT: X 15 GLU cc_start: 0.7696 (tt0) cc_final: 0.7491 (tt0) REVERT: X 36 LYS cc_start: 0.7843 (mttt) cc_final: 0.7574 (mtpt) REVERT: X 90 ASP cc_start: 0.8224 (t0) cc_final: 0.7986 (t0) REVERT: X 91 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7536 (tm-30) outliers start: 46 outliers final: 36 residues processed: 471 average time/residue: 0.1494 time to fit residues: 94.5299 Evaluate side-chains 480 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 443 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain H residue 59 ILE Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 56 THR Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain S residue 56 THR Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain U residue 56 THR Chi-restraints excluded: chain V residue 5 SER Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108199 restraints weight = 17880.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112017 restraints weight = 10242.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114672 restraints weight = 6736.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116490 restraints weight = 4833.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117913 restraints weight = 3695.338| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.132 Angle : 0.554 6.388 18810 Z= 0.301 Chirality : 0.035 0.145 1944 Planarity : 0.006 0.058 2412 Dihedral : 4.139 15.691 1800 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.60 % Allowed : 24.19 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1620 helix: 0.95 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.95 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 89 TYR 0.022 0.002 TYR M 32 PHE 0.012 0.001 PHE I 25 TRP 0.003 0.000 TRP H 68 HIS 0.009 0.002 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00323 (13968) covalent geometry : angle 0.55383 (18810) hydrogen bonds : bond 0.04111 ( 756) hydrogen bonds : angle 3.71854 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 441 time to evaluate : 0.535 Fit side-chains REVERT: G 81 ARG cc_start: 0.7904 (mmt180) cc_final: 0.6729 (mtp180) REVERT: G 90 ASP cc_start: 0.8087 (m-30) cc_final: 0.7490 (t0) REVERT: H 90 ASP cc_start: 0.8128 (t0) cc_final: 0.7634 (t0) REVERT: I 90 ASP cc_start: 0.8129 (t0) cc_final: 0.7654 (t0) REVERT: J 13 TYR cc_start: 0.8239 (m-10) cc_final: 0.7833 (m-10) REVERT: J 31 ASP cc_start: 0.8169 (m-30) cc_final: 0.7742 (m-30) REVERT: J 62 ASN cc_start: 0.8860 (m-40) cc_final: 0.8371 (m110) REVERT: J 70 MET cc_start: 0.8504 (ttp) cc_final: 0.8063 (ttm) REVERT: J 85 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7191 (tm-30) REVERT: K 13 TYR cc_start: 0.8340 (m-10) cc_final: 0.7965 (m-10) REVERT: K 16 ASP cc_start: 0.8704 (t0) cc_final: 0.8421 (t0) REVERT: K 50 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (t0) REVERT: K 62 ASN cc_start: 0.8799 (m110) cc_final: 0.8428 (m-40) REVERT: L 13 TYR cc_start: 0.8328 (m-10) cc_final: 0.7879 (m-10) REVERT: L 16 ASP cc_start: 0.8708 (t0) cc_final: 0.8380 (t0) REVERT: L 62 ASN cc_start: 0.8862 (m-40) cc_final: 0.8442 (m-40) REVERT: L 81 ARG cc_start: 0.7958 (mmt180) cc_final: 0.6547 (mtm110) REVERT: M 90 ASP cc_start: 0.7722 (t0) cc_final: 0.7482 (t0) REVERT: N 31 ASP cc_start: 0.8293 (m-30) cc_final: 0.7852 (m-30) REVERT: N 90 ASP cc_start: 0.7785 (t0) cc_final: 0.7343 (t0) REVERT: O 90 ASP cc_start: 0.7961 (t0) cc_final: 0.7459 (t0) REVERT: P 90 ASP cc_start: 0.7631 (t0) cc_final: 0.7277 (t0) REVERT: Q 62 ASN cc_start: 0.8677 (m-40) cc_final: 0.8408 (m110) REVERT: Q 90 ASP cc_start: 0.7956 (t0) cc_final: 0.7378 (t0) REVERT: R 62 ASN cc_start: 0.8846 (m-40) cc_final: 0.8125 (m-40) REVERT: R 90 ASP cc_start: 0.7614 (t0) cc_final: 0.7251 (t0) REVERT: S 31 ASP cc_start: 0.8045 (m-30) cc_final: 0.7836 (m-30) REVERT: S 85 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6651 (mt-10) REVERT: T 47 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6781 (mm-30) REVERT: U 30 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7343 (mt-10) REVERT: U 31 ASP cc_start: 0.8143 (m-30) cc_final: 0.7915 (m-30) REVERT: U 35 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7048 (tm-30) REVERT: U 47 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6833 (mm-30) REVERT: U 62 ASN cc_start: 0.9013 (m-40) cc_final: 0.8436 (m110) REVERT: U 90 ASP cc_start: 0.7836 (t0) cc_final: 0.7608 (t0) REVERT: V 27 MET cc_start: 0.8530 (ttp) cc_final: 0.8306 (ttt) REVERT: V 36 LYS cc_start: 0.7740 (mttt) cc_final: 0.7152 (mtpp) REVERT: V 62 ASN cc_start: 0.9005 (m-40) cc_final: 0.8656 (m-40) REVERT: W 12 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7468 (tpt90) REVERT: W 16 ASP cc_start: 0.8318 (t70) cc_final: 0.8054 (t0) REVERT: X 36 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7530 (mtpt) REVERT: X 90 ASP cc_start: 0.8234 (t0) cc_final: 0.7963 (t0) REVERT: X 91 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 37 outliers final: 28 residues processed: 455 average time/residue: 0.1499 time to fit residues: 91.8682 Evaluate side-chains 460 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 430 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 5 SER Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 56 THR Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 84 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 ASN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108539 restraints weight = 17901.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112419 restraints weight = 10285.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115075 restraints weight = 6742.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116901 restraints weight = 4829.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118313 restraints weight = 3702.500| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.135 Angle : 0.565 8.546 18810 Z= 0.306 Chirality : 0.035 0.151 1944 Planarity : 0.006 0.058 2412 Dihedral : 4.053 15.712 1800 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.32 % Allowed : 25.25 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1620 helix: 1.01 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.97 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 89 TYR 0.021 0.002 TYR M 32 PHE 0.016 0.001 PHE I 25 TRP 0.003 0.000 TRP R 68 HIS 0.009 0.002 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00331 (13968) covalent geometry : angle 0.56526 (18810) hydrogen bonds : bond 0.04077 ( 756) hydrogen bonds : angle 3.71919 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 431 time to evaluate : 0.412 Fit side-chains REVERT: G 81 ARG cc_start: 0.7903 (mmt180) cc_final: 0.6785 (mtp180) REVERT: G 90 ASP cc_start: 0.8106 (m-30) cc_final: 0.7546 (t0) REVERT: H 90 ASP cc_start: 0.8101 (t0) cc_final: 0.7609 (t0) REVERT: I 90 ASP cc_start: 0.8198 (t0) cc_final: 0.7728 (t0) REVERT: J 13 TYR cc_start: 0.8223 (m-10) cc_final: 0.7892 (m-10) REVERT: J 31 ASP cc_start: 0.8243 (m-30) cc_final: 0.7789 (m-30) REVERT: J 62 ASN cc_start: 0.8864 (m-40) cc_final: 0.8410 (m110) REVERT: J 70 MET cc_start: 0.8503 (ttp) cc_final: 0.7962 (ttm) REVERT: J 85 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7262 (tm-30) REVERT: J 90 ASP cc_start: 0.7187 (t0) cc_final: 0.6797 (t0) REVERT: K 13 TYR cc_start: 0.8335 (m-10) cc_final: 0.7942 (m-10) REVERT: K 16 ASP cc_start: 0.8701 (t0) cc_final: 0.8366 (t0) REVERT: K 50 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8404 (t0) REVERT: K 62 ASN cc_start: 0.8774 (m110) cc_final: 0.8423 (m-40) REVERT: L 13 TYR cc_start: 0.8294 (m-10) cc_final: 0.7939 (m-10) REVERT: L 16 ASP cc_start: 0.8712 (t0) cc_final: 0.8339 (t0) REVERT: L 62 ASN cc_start: 0.8881 (m-40) cc_final: 0.8425 (m110) REVERT: M 30 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7421 (mt-10) REVERT: M 90 ASP cc_start: 0.7814 (t0) cc_final: 0.7603 (t0) REVERT: N 31 ASP cc_start: 0.8221 (m-30) cc_final: 0.7819 (m-30) REVERT: N 90 ASP cc_start: 0.7748 (t0) cc_final: 0.7254 (t0) REVERT: O 90 ASP cc_start: 0.8031 (t0) cc_final: 0.7492 (t0) REVERT: P 90 ASP cc_start: 0.7643 (t0) cc_final: 0.7314 (t0) REVERT: Q 90 ASP cc_start: 0.7938 (t0) cc_final: 0.7375 (t0) REVERT: R 62 ASN cc_start: 0.8850 (m110) cc_final: 0.8635 (m-40) REVERT: R 90 ASP cc_start: 0.7673 (t0) cc_final: 0.7281 (t0) REVERT: S 85 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6629 (mt-10) REVERT: T 47 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6787 (mm-30) REVERT: U 31 ASP cc_start: 0.8138 (m-30) cc_final: 0.7927 (m-30) REVERT: U 35 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7057 (tm-30) REVERT: U 47 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6743 (mm-30) REVERT: U 62 ASN cc_start: 0.9011 (m-40) cc_final: 0.8440 (m110) REVERT: V 27 MET cc_start: 0.8470 (ttp) cc_final: 0.8237 (ttt) REVERT: V 36 LYS cc_start: 0.7698 (mttt) cc_final: 0.7115 (mtpp) REVERT: V 62 ASN cc_start: 0.9061 (m-40) cc_final: 0.8678 (m-40) REVERT: W 12 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7358 (tpt90) REVERT: W 16 ASP cc_start: 0.8271 (t70) cc_final: 0.7999 (t0) REVERT: X 36 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7410 (mtpt) REVERT: X 90 ASP cc_start: 0.8224 (t0) cc_final: 0.7958 (t0) REVERT: X 91 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7481 (tm-30) outliers start: 33 outliers final: 27 residues processed: 443 average time/residue: 0.1490 time to fit residues: 89.0269 Evaluate side-chains 456 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 427 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 HIS Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 5 SER Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108878 restraints weight = 17917.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112686 restraints weight = 10310.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115320 restraints weight = 6822.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117180 restraints weight = 4898.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118473 restraints weight = 3761.319| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13968 Z= 0.141 Angle : 0.582 10.530 18810 Z= 0.314 Chirality : 0.035 0.146 1944 Planarity : 0.006 0.064 2412 Dihedral : 4.048 16.060 1800 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.18 % Allowed : 25.25 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1620 helix: 1.01 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -0.98 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 89 TYR 0.020 0.002 TYR O 32 PHE 0.016 0.001 PHE I 25 TRP 0.004 0.000 TRP Q 68 HIS 0.009 0.002 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00348 (13968) covalent geometry : angle 0.58168 (18810) hydrogen bonds : bond 0.04101 ( 756) hydrogen bonds : angle 3.71569 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 435 time to evaluate : 0.529 Fit side-chains REVERT: G 81 ARG cc_start: 0.7915 (mmt180) cc_final: 0.6778 (mtp180) REVERT: G 90 ASP cc_start: 0.8116 (m-30) cc_final: 0.7592 (t0) REVERT: H 90 ASP cc_start: 0.8191 (t0) cc_final: 0.7695 (t0) REVERT: I 90 ASP cc_start: 0.8181 (t0) cc_final: 0.7769 (t0) REVERT: J 13 TYR cc_start: 0.8228 (m-10) cc_final: 0.7784 (m-10) REVERT: J 31 ASP cc_start: 0.8252 (m-30) cc_final: 0.7790 (m-30) REVERT: J 62 ASN cc_start: 0.8869 (m-40) cc_final: 0.8409 (m110) REVERT: J 85 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7220 (tm-30) REVERT: J 90 ASP cc_start: 0.7181 (t0) cc_final: 0.6780 (t0) REVERT: K 13 TYR cc_start: 0.8370 (m-10) cc_final: 0.7918 (m-10) REVERT: K 16 ASP cc_start: 0.8702 (t0) cc_final: 0.8361 (t0) REVERT: K 62 ASN cc_start: 0.8768 (m110) cc_final: 0.8343 (m-40) REVERT: K 90 ASP cc_start: 0.7245 (t0) cc_final: 0.6848 (t0) REVERT: L 13 TYR cc_start: 0.8291 (m-10) cc_final: 0.7897 (m-10) REVERT: L 16 ASP cc_start: 0.8675 (t0) cc_final: 0.8355 (t0) REVERT: L 62 ASN cc_start: 0.8887 (m-40) cc_final: 0.8420 (m110) REVERT: L 81 ARG cc_start: 0.7971 (mmt180) cc_final: 0.6578 (mtm110) REVERT: M 90 ASP cc_start: 0.7896 (t0) cc_final: 0.7656 (t0) REVERT: N 31 ASP cc_start: 0.8201 (m-30) cc_final: 0.7789 (m-30) REVERT: N 32 TYR cc_start: 0.9188 (t80) cc_final: 0.8918 (t80) REVERT: N 90 ASP cc_start: 0.7729 (t0) cc_final: 0.7263 (t0) REVERT: O 90 ASP cc_start: 0.8071 (t0) cc_final: 0.7530 (t0) REVERT: P 90 ASP cc_start: 0.7692 (t0) cc_final: 0.7375 (t0) REVERT: Q 90 ASP cc_start: 0.7954 (t0) cc_final: 0.7382 (t0) REVERT: R 62 ASN cc_start: 0.8854 (m110) cc_final: 0.8639 (m-40) REVERT: R 90 ASP cc_start: 0.7694 (t0) cc_final: 0.7312 (t0) REVERT: S 30 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6934 (tt0) REVERT: S 85 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6643 (mt-10) REVERT: T 90 ASP cc_start: 0.8052 (t0) cc_final: 0.7845 (t0) REVERT: U 3 MET cc_start: 0.7000 (pmm) cc_final: 0.6660 (ptt) REVERT: U 31 ASP cc_start: 0.8150 (m-30) cc_final: 0.7937 (m-30) REVERT: U 35 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7101 (tm-30) REVERT: U 47 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6747 (mm-30) REVERT: U 62 ASN cc_start: 0.9027 (m-40) cc_final: 0.8443 (m110) REVERT: V 27 MET cc_start: 0.8481 (ttp) cc_final: 0.8252 (ttt) REVERT: V 36 LYS cc_start: 0.7660 (mttt) cc_final: 0.7068 (mtpp) REVERT: V 62 ASN cc_start: 0.9063 (m-40) cc_final: 0.8685 (m-40) REVERT: W 12 ARG cc_start: 0.7637 (mmm160) cc_final: 0.7354 (tpt90) REVERT: W 16 ASP cc_start: 0.8274 (t70) cc_final: 0.7997 (t0) REVERT: X 36 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7145 (mtpp) REVERT: X 90 ASP cc_start: 0.8232 (t0) cc_final: 0.8013 (t0) REVERT: X 91 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 31 outliers final: 29 residues processed: 446 average time/residue: 0.1495 time to fit residues: 89.5432 Evaluate side-chains 459 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 429 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 17 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 5 SER Chi-restraints excluded: chain V residue 16 ASP Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain W residue 5 SER Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 36 LYS Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 45 GLN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112875 restraints weight = 17731.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116771 restraints weight = 10100.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119351 restraints weight = 6559.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121276 restraints weight = 4686.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122685 restraints weight = 3542.612| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13968 Z= 0.119 Angle : 0.562 10.223 18810 Z= 0.302 Chirality : 0.034 0.147 1944 Planarity : 0.006 0.064 2412 Dihedral : 3.860 16.607 1800 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.62 % Allowed : 26.02 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.20), residues: 1620 helix: 1.20 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.17 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 89 TYR 0.017 0.002 TYR J 32 PHE 0.014 0.001 PHE I 25 TRP 0.004 0.000 TRP Q 68 HIS 0.011 0.001 HIS U 51 Details of bonding type rmsd covalent geometry : bond 0.00289 (13968) covalent geometry : angle 0.56151 (18810) hydrogen bonds : bond 0.03520 ( 756) hydrogen bonds : angle 3.73177 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.81 seconds wall clock time: 39 minutes 34.42 seconds (2374.42 seconds total)