Starting phenix.real_space_refine on Sun Sep 29 22:56:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_13727_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_13727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_13727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_13727_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzd_13727/09_2024/7pzd_13727_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 3.52, per 1000 atoms: 0.26 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: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.23 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: 3.23 Time building geometry restraints manager: 4.05 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: 0.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.580 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- 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= 0.631 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP J 94 HIS 0.005 0.002 HIS G 28 PHE 0.019 0.004 PHE G 75 TYR 0.008 0.003 TYR W 13 ARG 0.014 0.001 ARG U 81 *********************** 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 fitting. rotamer outliers: 18 poor density : 549 time to evaluate : 1.621 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: 0.7617 (mtp-110) REVERT: H 81 ARG cc_start: 0.7385 (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: 0.8569 (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: 0.7451 (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: 0.8069 (mt-10) cc_final: 0.7834 (mt-10) REVERT: Q 62 ASN cc_start: 0.8840 (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: 0.7411 (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: 0.8197 (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: 0.3550 time to fit residues: 265.5944 Evaluate side-chains 473 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 463 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN H 51 HIS I 62 ASN J 28 HIS J 51 HIS K 28 HIS K 45 GLN K 51 HIS 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 51 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: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2888 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= 0.214 Angle : 0.625 6.045 18810 Z= 0.343 Chirality : 0.038 0.146 1944 Planarity : 0.005 0.037 2412 Dihedral : 4.900 30.332 1840 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.52 % Allowed : 18.85 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1620 helix: -0.13 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 73 HIS 0.008 0.003 HIS V 51 PHE 0.014 0.002 PHE G 25 TYR 0.022 0.002 TYR Q 32 ARG 0.008 0.001 ARG H 89 *********************** 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 519 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 469 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7439 (mmt180) cc_final: 0.7021 (ptt180) REVERT: I 81 ARG cc_start: 0.7256 (mmt180) cc_final: 0.6607 (ptt180) REVERT: I 90 ASP cc_start: 0.7128 (t0) cc_final: 0.6857 (t0) REVERT: J 13 TYR cc_start: 0.8357 (m-10) cc_final: 0.7903 (m-10) REVERT: J 31 ASP cc_start: 0.8190 (m-30) cc_final: 0.7741 (m-30) REVERT: J 62 ASN cc_start: 0.8867 (m-40) cc_final: 0.8350 (m-40) REVERT: J 90 ASP cc_start: 0.7115 (t0) cc_final: 0.6714 (t0) REVERT: K 13 TYR cc_start: 0.8338 (m-10) cc_final: 0.7956 (m-10) REVERT: K 31 ASP cc_start: 0.8245 (m-30) cc_final: 0.8012 (m-30) REVERT: K 62 ASN cc_start: 0.8845 (m-40) cc_final: 0.8452 (m-40) REVERT: K 70 MET cc_start: 0.8280 (mtm) cc_final: 0.8037 (mtm) REVERT: K 90 ASP cc_start: 0.7268 (t0) cc_final: 0.6804 (t0) REVERT: L 13 TYR cc_start: 0.8325 (m-10) cc_final: 0.7985 (m-10) REVERT: L 56 THR cc_start: 0.8654 (t) cc_final: 0.8388 (m) REVERT: L 62 ASN cc_start: 0.8868 (m-40) cc_final: 0.8419 (m-40) REVERT: L 81 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7028 (mtm110) REVERT: L 90 ASP cc_start: 0.7566 (t0) cc_final: 0.7207 (t0) REVERT: N 31 ASP cc_start: 0.8321 (m-30) cc_final: 0.7930 (m-30) REVERT: N 90 ASP cc_start: 0.7600 (t0) cc_final: 0.7253 (t0) REVERT: O 90 ASP cc_start: 0.7832 (t0) cc_final: 0.7363 (t0) REVERT: P 27 MET cc_start: 0.8394 (ttt) cc_final: 0.8013 (ttt) REVERT: P 31 ASP cc_start: 0.8461 (m-30) cc_final: 0.8224 (m-30) REVERT: P 47 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: P 90 ASP cc_start: 0.7693 (t0) cc_final: 0.7229 (t0) REVERT: Q 31 ASP cc_start: 0.8263 (m-30) cc_final: 0.8054 (m-30) REVERT: Q 62 ASN cc_start: 0.8617 (m-40) cc_final: 0.8299 (m110) REVERT: Q 90 ASP cc_start: 0.7937 (t0) cc_final: 0.7420 (t0) REVERT: R 62 ASN cc_start: 0.8613 (m-40) cc_final: 0.7936 (m110) REVERT: R 90 ASP cc_start: 0.7705 (t0) cc_final: 0.7356 (t0) REVERT: T 30 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7415 (mt-10) REVERT: T 90 ASP cc_start: 0.8061 (t0) cc_final: 0.7800 (t0) REVERT: U 30 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7315 (mt-10) REVERT: U 31 ASP cc_start: 0.8020 (m-30) cc_final: 0.7803 (m-30) REVERT: U 47 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6651 (mm-30) REVERT: U 62 ASN cc_start: 0.8861 (m-40) cc_final: 0.8377 (m110) REVERT: U 90 ASP cc_start: 0.7802 (t0) cc_final: 0.7595 (t0) REVERT: V 36 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7181 (mtpp) REVERT: V 62 ASN cc_start: 0.9016 (m-40) cc_final: 0.8712 (m-40) REVERT: V 85 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7405 (mt-10) REVERT: W 16 ASP cc_start: 0.8481 (t0) cc_final: 0.8001 (t0) REVERT: W 90 ASP cc_start: 0.7769 (t0) cc_final: 0.7487 (t0) outliers start: 50 outliers final: 25 residues processed: 492 average time/residue: 0.3144 time to fit residues: 207.5323 Evaluate side-chains 467 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 440 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 10 LEU Chi-restraints excluded: chain J residue 47 GLU 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 L residue 86 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 P residue 47 GLU Chi-restraints excluded: chain S residue 51 HIS 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 88 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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** J 45 GLN N 45 GLN P 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.005 0.042 13968 Z= 0.337 Angle : 0.629 6.386 18810 Z= 0.341 Chirality : 0.040 0.162 1944 Planarity : 0.006 0.042 2412 Dihedral : 4.409 15.201 1800 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.88 % Allowed : 20.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1620 helix: 0.20 (0.14), residues: 1278 sheet: None (None), residues: 0 loop : -0.95 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 73 HIS 0.013 0.003 HIS H 51 PHE 0.015 0.002 PHE G 25 TYR 0.022 0.002 TYR J 84 ARG 0.008 0.001 ARG K 89 *********************** 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 496 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 455 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7574 (mmt180) cc_final: 0.6980 (ptp-170) REVERT: I 81 ARG cc_start: 0.7344 (mmt180) cc_final: 0.6596 (ptp-170) REVERT: I 90 ASP cc_start: 0.7494 (t0) cc_final: 0.7142 (t0) REVERT: J 13 TYR cc_start: 0.8428 (m-10) cc_final: 0.8079 (m-10) REVERT: J 31 ASP cc_start: 0.8247 (m-30) cc_final: 0.7857 (m-30) REVERT: J 62 ASN cc_start: 0.8953 (m-40) cc_final: 0.8500 (m-40) REVERT: J 90 ASP cc_start: 0.7228 (t0) cc_final: 0.6932 (t0) REVERT: K 13 TYR cc_start: 0.8433 (m-10) cc_final: 0.7966 (m-10) REVERT: K 62 ASN cc_start: 0.8911 (m-40) cc_final: 0.8246 (m-40) REVERT: K 70 MET cc_start: 0.8352 (mtm) cc_final: 0.8146 (mtm) REVERT: K 89 ARG cc_start: 0.8209 (mtm110) cc_final: 0.7974 (mtm110) REVERT: K 90 ASP cc_start: 0.7332 (t0) cc_final: 0.6868 (t0) REVERT: L 13 TYR cc_start: 0.8490 (m-10) cc_final: 0.8070 (m-10) REVERT: L 62 ASN cc_start: 0.8946 (m-40) cc_final: 0.8630 (m-40) REVERT: L 81 ARG cc_start: 0.7936 (mmt180) cc_final: 0.6782 (mtm180) REVERT: N 31 ASP cc_start: 0.8277 (m-30) cc_final: 0.7930 (m-30) REVERT: N 90 ASP cc_start: 0.7842 (t0) cc_final: 0.7384 (t0) REVERT: O 17 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8726 (mp) REVERT: O 90 ASP cc_start: 0.7964 (t0) cc_final: 0.7448 (t0) REVERT: P 27 MET cc_start: 0.8511 (ttp) cc_final: 0.8172 (ttt) REVERT: P 90 ASP cc_start: 0.7645 (t0) cc_final: 0.7262 (t0) REVERT: Q 62 ASN cc_start: 0.8785 (m-40) cc_final: 0.8417 (m-40) REVERT: Q 90 ASP cc_start: 0.8015 (t0) cc_final: 0.7637 (t0) REVERT: R 62 ASN cc_start: 0.8837 (m-40) cc_final: 0.8182 (m110) REVERT: R 90 ASP cc_start: 0.7586 (t0) cc_final: 0.7211 (t0) REVERT: S 27 MET cc_start: 0.8687 (ttp) cc_final: 0.8445 (ttt) REVERT: S 47 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7037 (mm-30) REVERT: T 47 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7198 (mm-30) REVERT: T 90 ASP cc_start: 0.8016 (t0) cc_final: 0.7743 (t0) REVERT: U 31 ASP cc_start: 0.8124 (m-30) cc_final: 0.7859 (m-30) REVERT: U 35 GLN cc_start: 0.7357 (tm-30) cc_final: 0.7127 (tm-30) REVERT: U 47 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6843 (mm-30) REVERT: U 62 ASN cc_start: 0.9115 (m-40) cc_final: 0.8531 (m-40) REVERT: V 32 TYR cc_start: 0.8446 (t80) cc_final: 0.8168 (t80) REVERT: V 36 LYS cc_start: 0.7756 (mttt) cc_final: 0.7306 (mtpp) REVERT: V 62 ASN cc_start: 0.9246 (m-40) cc_final: 0.8905 (m-40) REVERT: W 16 ASP cc_start: 0.8508 (t70) cc_final: 0.8062 (t0) REVERT: W 36 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7038 (mtpp) REVERT: W 70 MET cc_start: 0.8036 (mtp) cc_final: 0.7775 (mtp) REVERT: X 15 GLU cc_start: 0.7663 (tt0) cc_final: 0.7388 (tt0) outliers start: 41 outliers final: 31 residues processed: 472 average time/residue: 0.3221 time to fit residues: 203.0690 Evaluate side-chains 466 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 434 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 27 MET Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 27 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain M residue 56 THR 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 17 LEU Chi-restraints excluded: chain O residue 58 MET 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 X residue 16 ASP 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 145 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 50.0000 chunk 156 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 45 GLN S 51 HIS V 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3790 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= 0.191 Angle : 0.551 6.111 18810 Z= 0.297 Chirality : 0.035 0.150 1944 Planarity : 0.005 0.045 2412 Dihedral : 4.143 15.610 1800 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.95 % Allowed : 22.86 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1620 helix: 0.50 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP H 68 HIS 0.007 0.001 HIS I 51 PHE 0.012 0.002 PHE H 25 TYR 0.019 0.002 TYR O 32 ARG 0.009 0.001 ARG L 89 *********************** 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 486 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 444 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7550 (mmt180) cc_final: 0.6968 (ptp-170) REVERT: G 90 ASP cc_start: 0.7142 (t0) cc_final: 0.6850 (t0) REVERT: H 90 ASP cc_start: 0.7558 (t0) cc_final: 0.7230 (t0) REVERT: I 81 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6496 (ptp-170) REVERT: I 90 ASP cc_start: 0.7509 (t0) cc_final: 0.7198 (t0) REVERT: J 13 TYR cc_start: 0.8381 (m-10) cc_final: 0.7972 (m-10) REVERT: J 31 ASP cc_start: 0.8125 (m-30) cc_final: 0.7747 (m-30) REVERT: J 62 ASN cc_start: 0.8848 (m-40) cc_final: 0.8385 (m110) REVERT: J 90 ASP cc_start: 0.7223 (t0) cc_final: 0.6803 (t0) REVERT: K 13 TYR cc_start: 0.8379 (m-10) cc_final: 0.8042 (m-10) REVERT: K 62 ASN cc_start: 0.8776 (m-40) cc_final: 0.8075 (m-40) REVERT: K 70 MET cc_start: 0.8360 (mtm) cc_final: 0.8138 (mtm) REVERT: K 90 ASP cc_start: 0.7186 (t0) cc_final: 0.6763 (t0) REVERT: L 13 TYR cc_start: 0.8414 (m-10) cc_final: 0.8052 (m-10) REVERT: L 62 ASN cc_start: 0.8804 (m-40) cc_final: 0.8468 (m-40) REVERT: L 81 ARG cc_start: 0.7826 (mmt180) cc_final: 0.6611 (mtm110) REVERT: M 90 ASP cc_start: 0.7371 (t0) cc_final: 0.7112 (t0) REVERT: N 31 ASP cc_start: 0.8225 (m-30) cc_final: 0.7863 (m-30) REVERT: N 90 ASP cc_start: 0.7801 (t0) cc_final: 0.7352 (t0) REVERT: O 90 ASP cc_start: 0.7902 (t0) cc_final: 0.7420 (t0) REVERT: P 27 MET cc_start: 0.8398 (ttp) cc_final: 0.8135 (ttt) REVERT: P 90 ASP cc_start: 0.7583 (t0) cc_final: 0.7221 (t0) REVERT: Q 62 ASN cc_start: 0.8673 (m-40) cc_final: 0.8385 (m110) REVERT: Q 90 ASP cc_start: 0.7928 (t0) cc_final: 0.7360 (t0) REVERT: R 62 ASN cc_start: 0.8683 (m-40) cc_final: 0.8059 (m110) REVERT: R 90 ASP cc_start: 0.7476 (t0) cc_final: 0.7091 (t0) REVERT: S 27 MET cc_start: 0.8624 (ttp) cc_final: 0.8385 (ttt) REVERT: S 31 ASP cc_start: 0.7978 (m-30) cc_final: 0.7754 (m-30) REVERT: S 85 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6652 (mt-10) REVERT: T 47 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7015 (mm-30) REVERT: U 31 ASP cc_start: 0.8015 (m-30) cc_final: 0.7718 (m-30) REVERT: U 62 ASN cc_start: 0.8992 (m-40) cc_final: 0.8501 (m-40) REVERT: U 90 ASP cc_start: 0.7698 (t0) cc_final: 0.7421 (t0) REVERT: V 32 TYR cc_start: 0.8428 (t80) cc_final: 0.8197 (t80) REVERT: V 36 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7233 (mtpp) REVERT: V 62 ASN cc_start: 0.9074 (m-40) cc_final: 0.8735 (m-40) REVERT: V 90 ASP cc_start: 0.8223 (t0) cc_final: 0.7955 (t0) REVERT: W 12 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7399 (tpt90) REVERT: W 16 ASP cc_start: 0.8507 (t70) cc_final: 0.8119 (t0) REVERT: W 36 LYS cc_start: 0.7582 (mtpt) cc_final: 0.7025 (mtpp) REVERT: W 70 MET cc_start: 0.7983 (mtp) cc_final: 0.7778 (mtp) REVERT: W 91 GLU cc_start: 0.7959 (tt0) cc_final: 0.7636 (tt0) REVERT: X 90 ASP cc_start: 0.8163 (t0) cc_final: 0.7952 (t0) outliers start: 42 outliers final: 25 residues processed: 463 average time/residue: 0.3289 time to fit residues: 204.4195 Evaluate side-chains 456 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 430 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain K residue 10 LEU 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 14 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 88 LYS 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 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 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP 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 130 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 140 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3974 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= 0.208 Angle : 0.549 6.350 18810 Z= 0.298 Chirality : 0.035 0.153 1944 Planarity : 0.005 0.046 2412 Dihedral : 4.066 15.641 1800 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.95 % Allowed : 22.50 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1620 helix: 0.71 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 68 HIS 0.007 0.001 HIS G 51 PHE 0.016 0.001 PHE H 25 TYR 0.027 0.002 TYR M 32 ARG 0.010 0.001 ARG K 89 *********************** 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 479 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 437 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7532 (mmt180) cc_final: 0.6903 (mtp180) REVERT: G 90 ASP cc_start: 0.7264 (t0) cc_final: 0.6858 (t0) REVERT: H 90 ASP cc_start: 0.7567 (t0) cc_final: 0.7136 (t0) REVERT: I 81 ARG cc_start: 0.7280 (mmt180) cc_final: 0.6430 (ptp-170) REVERT: I 90 ASP cc_start: 0.7673 (t0) cc_final: 0.7364 (t0) REVERT: J 13 TYR cc_start: 0.8349 (m-10) cc_final: 0.8008 (m-10) REVERT: J 31 ASP cc_start: 0.8150 (m-30) cc_final: 0.7750 (m-30) REVERT: J 62 ASN cc_start: 0.8876 (m-40) cc_final: 0.8424 (m110) REVERT: J 90 ASP cc_start: 0.7230 (t0) cc_final: 0.6783 (t0) REVERT: K 13 TYR cc_start: 0.8430 (m-10) cc_final: 0.8013 (m-10) REVERT: K 62 ASN cc_start: 0.8768 (m-40) cc_final: 0.8073 (m-40) REVERT: K 90 ASP cc_start: 0.7288 (t0) cc_final: 0.6842 (t0) REVERT: L 13 TYR cc_start: 0.8436 (m-10) cc_final: 0.7984 (m-10) REVERT: L 62 ASN cc_start: 0.8819 (m-40) cc_final: 0.8485 (m-40) REVERT: M 90 ASP cc_start: 0.7573 (t0) cc_final: 0.7355 (t0) REVERT: N 31 ASP cc_start: 0.8209 (m-30) cc_final: 0.7866 (m-30) REVERT: N 90 ASP cc_start: 0.7779 (t0) cc_final: 0.7354 (t0) REVERT: O 90 ASP cc_start: 0.7906 (t0) cc_final: 0.7417 (t0) REVERT: P 90 ASP cc_start: 0.7628 (t0) cc_final: 0.7231 (t0) REVERT: Q 62 ASN cc_start: 0.8750 (m-40) cc_final: 0.8429 (m110) REVERT: Q 90 ASP cc_start: 0.7973 (t0) cc_final: 0.7438 (t0) REVERT: R 62 ASN cc_start: 0.8699 (m-40) cc_final: 0.8032 (m110) REVERT: R 90 ASP cc_start: 0.7555 (t0) cc_final: 0.7162 (t0) REVERT: S 27 MET cc_start: 0.8597 (ttp) cc_final: 0.8389 (ttt) REVERT: S 85 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6622 (mt-10) REVERT: S 90 ASP cc_start: 0.7977 (t0) cc_final: 0.7774 (t0) REVERT: T 30 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7540 (mt-10) REVERT: T 47 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7056 (mm-30) REVERT: U 30 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7439 (mt-10) REVERT: U 31 ASP cc_start: 0.8026 (m-30) cc_final: 0.7685 (m-30) REVERT: U 35 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6972 (tm-30) REVERT: U 62 ASN cc_start: 0.9022 (m-40) cc_final: 0.8554 (m-40) REVERT: U 90 ASP cc_start: 0.7791 (t0) cc_final: 0.7576 (t0) REVERT: V 27 MET cc_start: 0.8569 (ttp) cc_final: 0.8315 (ttt) REVERT: V 32 TYR cc_start: 0.8447 (t80) cc_final: 0.8234 (t80) REVERT: V 36 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7250 (mtpp) REVERT: V 62 ASN cc_start: 0.9114 (m-40) cc_final: 0.8763 (m-40) REVERT: V 90 ASP cc_start: 0.8316 (t0) cc_final: 0.8024 (t0) REVERT: W 12 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7361 (tpt90) REVERT: W 36 LYS cc_start: 0.7501 (mtpt) cc_final: 0.7173 (mtpt) REVERT: W 91 GLU cc_start: 0.8012 (tt0) cc_final: 0.7673 (tt0) REVERT: X 90 ASP cc_start: 0.8217 (t0) cc_final: 0.7954 (t0) REVERT: X 91 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7409 (tm-30) outliers start: 42 outliers final: 32 residues processed: 458 average time/residue: 0.3266 time to fit residues: 200.7552 Evaluate side-chains 465 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 432 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 LEU 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 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 88 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 14 LEU Chi-restraints excluded: chain O residue 56 THR 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 56 THR Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 27 MET 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 47 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 56 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 156 optimal weight: 40.0000 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13968 Z= 0.247 Angle : 0.564 6.290 18810 Z= 0.306 Chirality : 0.036 0.148 1944 Planarity : 0.005 0.047 2412 Dihedral : 4.137 15.678 1800 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.52 % Allowed : 22.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1620 helix: 0.87 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 73 HIS 0.008 0.002 HIS G 51 PHE 0.013 0.001 PHE H 25 TYR 0.025 0.002 TYR M 32 ARG 0.011 0.001 ARG K 89 *********************** 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 483 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 433 time to evaluate : 1.755 Fit side-chains REVERT: G 81 ARG cc_start: 0.7498 (mmt180) cc_final: 0.6834 (mtp180) REVERT: G 90 ASP cc_start: 0.7397 (t0) cc_final: 0.6983 (t0) REVERT: H 90 ASP cc_start: 0.7630 (t0) cc_final: 0.7150 (t0) REVERT: I 81 ARG cc_start: 0.7282 (mmt180) cc_final: 0.6439 (ptp-170) REVERT: I 90 ASP cc_start: 0.7758 (t0) cc_final: 0.7441 (t0) REVERT: J 13 TYR cc_start: 0.8388 (m-10) cc_final: 0.8080 (m-10) REVERT: J 31 ASP cc_start: 0.8203 (m-30) cc_final: 0.7809 (m-30) REVERT: J 62 ASN cc_start: 0.8856 (m-40) cc_final: 0.8432 (m110) REVERT: J 70 MET cc_start: 0.8045 (mtp) cc_final: 0.7777 (ttm) REVERT: K 13 TYR cc_start: 0.8484 (m-10) cc_final: 0.7960 (m-10) REVERT: K 62 ASN cc_start: 0.8846 (m-40) cc_final: 0.8447 (m-40) REVERT: K 90 ASP cc_start: 0.7375 (t0) cc_final: 0.6929 (t0) REVERT: L 13 TYR cc_start: 0.8451 (m-10) cc_final: 0.8018 (m-10) REVERT: L 62 ASN cc_start: 0.8842 (m-40) cc_final: 0.8475 (m-40) REVERT: M 90 ASP cc_start: 0.7599 (t0) cc_final: 0.7365 (t0) REVERT: N 31 ASP cc_start: 0.8194 (m-30) cc_final: 0.7806 (m-30) REVERT: N 90 ASP cc_start: 0.7863 (t0) cc_final: 0.7422 (t0) REVERT: O 90 ASP cc_start: 0.7967 (t0) cc_final: 0.7448 (t0) REVERT: P 90 ASP cc_start: 0.7669 (t0) cc_final: 0.7283 (t0) REVERT: Q 62 ASN cc_start: 0.8787 (m-40) cc_final: 0.8472 (m110) REVERT: Q 90 ASP cc_start: 0.7989 (t0) cc_final: 0.7386 (t0) REVERT: R 62 ASN cc_start: 0.8754 (m-40) cc_final: 0.8051 (m110) REVERT: R 90 ASP cc_start: 0.7599 (t0) cc_final: 0.7206 (t0) REVERT: S 27 MET cc_start: 0.8603 (ttp) cc_final: 0.8390 (ttt) REVERT: S 85 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6590 (mt-10) REVERT: T 47 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6984 (mm-30) REVERT: U 31 ASP cc_start: 0.8055 (m-30) cc_final: 0.7687 (m-30) REVERT: U 35 GLN cc_start: 0.7347 (tm-30) cc_final: 0.6959 (tm-30) REVERT: U 62 ASN cc_start: 0.9014 (m-40) cc_final: 0.8577 (m-40) REVERT: V 27 MET cc_start: 0.8562 (ttp) cc_final: 0.8305 (ttt) REVERT: V 32 TYR cc_start: 0.8573 (t80) cc_final: 0.8363 (t80) REVERT: V 36 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7297 (mtpp) REVERT: V 62 ASN cc_start: 0.9210 (m-40) cc_final: 0.8829 (m-40) REVERT: V 90 ASP cc_start: 0.8342 (t0) cc_final: 0.8029 (t0) REVERT: W 12 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7367 (tpt90) REVERT: W 36 LYS cc_start: 0.7508 (mtpt) cc_final: 0.6930 (mtpp) REVERT: X 90 ASP cc_start: 0.8267 (t0) cc_final: 0.7980 (t0) REVERT: X 91 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7440 (tm-30) outliers start: 50 outliers final: 37 residues processed: 460 average time/residue: 0.3224 time to fit residues: 199.5849 Evaluate side-chains 469 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 431 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 15 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 88 LYS Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain O residue 10 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 27 MET 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 5 SER Chi-restraints excluded: chain W residue 47 GLU 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 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 151 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4297 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= 0.188 Angle : 0.545 6.085 18810 Z= 0.295 Chirality : 0.035 0.140 1944 Planarity : 0.005 0.053 2412 Dihedral : 3.989 15.527 1800 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.46 % Allowed : 24.19 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1620 helix: 1.09 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.89 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 68 HIS 0.008 0.001 HIS G 51 PHE 0.012 0.001 PHE H 25 TYR 0.021 0.002 TYR M 32 ARG 0.013 0.001 ARG K 89 *********************** 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 464 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 429 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7486 (mmt180) cc_final: 0.6927 (mtp180) REVERT: G 90 ASP cc_start: 0.7557 (t0) cc_final: 0.7109 (t0) REVERT: H 90 ASP cc_start: 0.7731 (t0) cc_final: 0.7321 (t0) REVERT: I 90 ASP cc_start: 0.7806 (t0) cc_final: 0.7372 (t0) REVERT: J 13 TYR cc_start: 0.8347 (m-10) cc_final: 0.7967 (m-10) REVERT: J 31 ASP cc_start: 0.8138 (m-30) cc_final: 0.7760 (m-30) REVERT: J 62 ASN cc_start: 0.8798 (m-40) cc_final: 0.8383 (m110) REVERT: J 70 MET cc_start: 0.8056 (mtp) cc_final: 0.7717 (ttm) REVERT: K 13 TYR cc_start: 0.8468 (m-10) cc_final: 0.8031 (m-10) REVERT: K 62 ASN cc_start: 0.8786 (m-40) cc_final: 0.8448 (m-40) REVERT: K 90 ASP cc_start: 0.7224 (t0) cc_final: 0.6808 (t0) REVERT: L 13 TYR cc_start: 0.8450 (m-10) cc_final: 0.8046 (m-10) REVERT: L 62 ASN cc_start: 0.8787 (m-40) cc_final: 0.8444 (m-40) REVERT: M 90 ASP cc_start: 0.7578 (t0) cc_final: 0.7369 (t0) REVERT: N 31 ASP cc_start: 0.8159 (m-30) cc_final: 0.7778 (m-30) REVERT: N 90 ASP cc_start: 0.7639 (t0) cc_final: 0.7280 (t0) REVERT: O 90 ASP cc_start: 0.7897 (t0) cc_final: 0.7410 (t0) REVERT: P 90 ASP cc_start: 0.7545 (t0) cc_final: 0.7128 (t0) REVERT: Q 31 ASP cc_start: 0.8206 (m-30) cc_final: 0.7993 (m-30) REVERT: Q 62 ASN cc_start: 0.8629 (m-40) cc_final: 0.8359 (m110) REVERT: Q 90 ASP cc_start: 0.7958 (t0) cc_final: 0.7400 (t0) REVERT: R 62 ASN cc_start: 0.8636 (m-40) cc_final: 0.7951 (m110) REVERT: R 90 ASP cc_start: 0.7559 (t0) cc_final: 0.7176 (t0) REVERT: S 47 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6756 (mm-30) REVERT: S 85 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6613 (mt-10) REVERT: S 90 ASP cc_start: 0.8016 (t0) cc_final: 0.7654 (t0) REVERT: T 47 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7072 (mm-30) REVERT: U 31 ASP cc_start: 0.8000 (m-30) cc_final: 0.7634 (m-30) REVERT: U 35 GLN cc_start: 0.7303 (tm-30) cc_final: 0.6917 (tm-30) REVERT: U 62 ASN cc_start: 0.8950 (m-40) cc_final: 0.8570 (m-40) REVERT: U 90 ASP cc_start: 0.7845 (t0) cc_final: 0.7469 (t0) REVERT: V 36 LYS cc_start: 0.7794 (mttt) cc_final: 0.7263 (mtpp) REVERT: V 62 ASN cc_start: 0.9030 (m-40) cc_final: 0.8671 (m-40) REVERT: V 90 ASP cc_start: 0.8296 (t0) cc_final: 0.8063 (t0) REVERT: W 12 ARG cc_start: 0.7552 (mmm160) cc_final: 0.7307 (tpt90) REVERT: W 36 LYS cc_start: 0.7509 (mtpt) cc_final: 0.6976 (mtpp) REVERT: X 90 ASP cc_start: 0.8268 (t0) cc_final: 0.8043 (t0) REVERT: X 91 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7044 (tm-30) outliers start: 35 outliers final: 26 residues processed: 444 average time/residue: 0.3231 time to fit residues: 192.4296 Evaluate side-chains 446 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 420 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 14 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 17 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain S residue 15 GLU 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 10 LEU Chi-restraints excluded: chain V residue 47 GLU 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 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 122 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN X 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13968 Z= 0.271 Angle : 0.590 6.678 18810 Z= 0.321 Chirality : 0.037 0.175 1944 Planarity : 0.006 0.056 2412 Dihedral : 4.144 15.656 1800 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.88 % Allowed : 24.33 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1620 helix: 1.06 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.18 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 68 HIS 0.009 0.002 HIS U 51 PHE 0.017 0.001 PHE I 25 TYR 0.025 0.002 TYR U 32 ARG 0.014 0.001 ARG K 89 *********************** 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 475 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 434 time to evaluate : 1.747 Fit side-chains REVERT: G 81 ARG cc_start: 0.7472 (mmt180) cc_final: 0.6881 (mtp180) REVERT: G 90 ASP cc_start: 0.7782 (t0) cc_final: 0.7320 (t0) REVERT: H 90 ASP cc_start: 0.7799 (t0) cc_final: 0.7327 (t0) REVERT: I 3 MET cc_start: 0.7818 (ptt) cc_final: 0.7461 (ttp) REVERT: I 90 ASP cc_start: 0.7828 (t0) cc_final: 0.7372 (t0) REVERT: J 13 TYR cc_start: 0.8376 (m-10) cc_final: 0.8024 (m-10) REVERT: J 31 ASP cc_start: 0.8231 (m-30) cc_final: 0.7838 (m-30) REVERT: J 62 ASN cc_start: 0.8845 (m-40) cc_final: 0.8461 (m-40) REVERT: K 13 TYR cc_start: 0.8510 (m-10) cc_final: 0.8032 (m-10) REVERT: K 62 ASN cc_start: 0.8882 (m-40) cc_final: 0.8423 (m-40) REVERT: K 90 ASP cc_start: 0.7274 (t0) cc_final: 0.6926 (t0) REVERT: L 13 TYR cc_start: 0.8504 (m-10) cc_final: 0.7999 (m-10) REVERT: L 62 ASN cc_start: 0.8838 (m-40) cc_final: 0.8461 (m-40) REVERT: M 90 ASP cc_start: 0.7714 (t0) cc_final: 0.7501 (t0) REVERT: N 31 ASP cc_start: 0.8162 (m-30) cc_final: 0.7788 (m-30) REVERT: N 90 ASP cc_start: 0.7790 (t0) cc_final: 0.7398 (t0) REVERT: O 90 ASP cc_start: 0.7965 (t0) cc_final: 0.7473 (t0) REVERT: P 90 ASP cc_start: 0.7656 (t0) cc_final: 0.7300 (t0) REVERT: Q 62 ASN cc_start: 0.8792 (m-40) cc_final: 0.8501 (m110) REVERT: Q 90 ASP cc_start: 0.8023 (t0) cc_final: 0.7596 (t0) REVERT: R 62 ASN cc_start: 0.8745 (m-40) cc_final: 0.8038 (m110) REVERT: R 90 ASP cc_start: 0.7656 (t0) cc_final: 0.7267 (t0) REVERT: S 85 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6554 (mt-10) REVERT: T 47 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6942 (mm-30) REVERT: T 90 ASP cc_start: 0.8050 (t0) cc_final: 0.7837 (t0) REVERT: U 31 ASP cc_start: 0.8018 (m-30) cc_final: 0.7665 (m-30) REVERT: U 35 GLN cc_start: 0.7295 (tm-30) cc_final: 0.6919 (tm-30) REVERT: U 62 ASN cc_start: 0.9012 (m110) cc_final: 0.8642 (m-40) REVERT: U 90 ASP cc_start: 0.7916 (t0) cc_final: 0.7629 (t0) REVERT: V 27 MET cc_start: 0.8479 (ttp) cc_final: 0.8236 (ttt) REVERT: V 36 LYS cc_start: 0.7972 (mttt) cc_final: 0.7433 (mtpp) REVERT: V 62 ASN cc_start: 0.9163 (m-40) cc_final: 0.8885 (m-40) REVERT: V 90 ASP cc_start: 0.8333 (t0) cc_final: 0.8043 (t0) REVERT: W 12 ARG cc_start: 0.7611 (mmm160) cc_final: 0.7362 (tpt90) REVERT: W 36 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7336 (mtpt) REVERT: W 90 ASP cc_start: 0.8008 (t0) cc_final: 0.7753 (t0) REVERT: X 15 GLU cc_start: 0.7609 (tt0) cc_final: 0.7329 (tt0) REVERT: X 90 ASP cc_start: 0.8328 (t0) cc_final: 0.8086 (t0) REVERT: X 91 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7175 (tm-30) outliers start: 41 outliers final: 31 residues processed: 453 average time/residue: 0.3259 time to fit residues: 197.2600 Evaluate side-chains 462 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 431 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 J residue 27 MET Chi-restraints excluded: chain K residue 15 GLU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L 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 56 THR Chi-restraints excluded: chain O residue 88 LYS Chi-restraints excluded: chain Q residue 5 SER 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 10 LEU 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 47 GLU Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 16 ASP 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 149 optimal weight: 0.0770 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4493 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= 0.184 Angle : 0.561 7.495 18810 Z= 0.303 Chirality : 0.035 0.175 1944 Planarity : 0.005 0.060 2412 Dihedral : 3.939 15.371 1800 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.69 % Allowed : 25.53 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1620 helix: 1.18 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -1.00 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP L 73 HIS 0.009 0.001 HIS G 51 PHE 0.013 0.001 PHE I 25 TYR 0.024 0.002 TYR L 84 ARG 0.014 0.001 ARG K 89 *********************** 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 fitting. rotamer outliers: 24 poor density : 440 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: G 81 ARG cc_start: 0.7466 (mmt180) cc_final: 0.6935 (mtp180) REVERT: G 90 ASP cc_start: 0.7743 (t0) cc_final: 0.7297 (t0) REVERT: H 90 ASP cc_start: 0.7706 (t0) cc_final: 0.7257 (t0) REVERT: I 90 ASP cc_start: 0.7810 (t0) cc_final: 0.7433 (t0) REVERT: J 13 TYR cc_start: 0.8317 (m-10) cc_final: 0.7956 (m-10) REVERT: J 31 ASP cc_start: 0.8180 (m-30) cc_final: 0.7794 (m-30) REVERT: J 62 ASN cc_start: 0.8800 (m-40) cc_final: 0.8360 (m110) REVERT: K 13 TYR cc_start: 0.8465 (m-10) cc_final: 0.8033 (m-10) REVERT: K 62 ASN cc_start: 0.8795 (m-40) cc_final: 0.8301 (m-40) REVERT: K 90 ASP cc_start: 0.7072 (t0) cc_final: 0.6831 (t0) REVERT: L 13 TYR cc_start: 0.8487 (m-10) cc_final: 0.8079 (m-10) REVERT: L 62 ASN cc_start: 0.8771 (m-40) cc_final: 0.8394 (m-40) REVERT: N 31 ASP cc_start: 0.8130 (m-30) cc_final: 0.7772 (m-30) REVERT: N 90 ASP cc_start: 0.7650 (t0) cc_final: 0.7291 (t0) REVERT: O 90 ASP cc_start: 0.7894 (t0) cc_final: 0.7401 (t0) REVERT: P 90 ASP cc_start: 0.7584 (t0) cc_final: 0.7188 (t0) REVERT: Q 62 ASN cc_start: 0.8594 (m-40) cc_final: 0.8323 (m110) REVERT: Q 90 ASP cc_start: 0.7937 (t0) cc_final: 0.7356 (t0) REVERT: R 62 ASN cc_start: 0.8605 (m-40) cc_final: 0.7930 (m110) REVERT: R 90 ASP cc_start: 0.7580 (t0) cc_final: 0.7246 (t0) REVERT: S 47 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6807 (mm-30) REVERT: S 85 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6565 (mt-10) REVERT: S 90 ASP cc_start: 0.8009 (t0) cc_final: 0.7773 (t0) REVERT: T 47 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7107 (mm-30) REVERT: U 31 ASP cc_start: 0.7970 (m-30) cc_final: 0.7589 (m-30) REVERT: U 62 ASN cc_start: 0.8912 (m110) cc_final: 0.8602 (m-40) REVERT: U 90 ASP cc_start: 0.7776 (t0) cc_final: 0.7549 (t0) REVERT: V 27 MET cc_start: 0.8415 (ttp) cc_final: 0.8154 (ttt) REVERT: V 36 LYS cc_start: 0.7639 (mttt) cc_final: 0.7134 (mtpp) REVERT: W 12 ARG cc_start: 0.7550 (mmm160) cc_final: 0.7320 (tpt90) REVERT: W 36 LYS cc_start: 0.7545 (mtpt) cc_final: 0.6967 (mtpp) outliers start: 24 outliers final: 17 residues processed: 447 average time/residue: 0.3310 time to fit residues: 197.1338 Evaluate side-chains 444 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 427 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 17 LEU 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 U residue 17 LEU Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 47 GLU 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 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13968 Z= 0.300 Angle : 0.631 8.128 18810 Z= 0.343 Chirality : 0.038 0.188 1944 Planarity : 0.006 0.061 2412 Dihedral : 4.128 15.456 1800 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.97 % Allowed : 25.81 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1620 helix: 0.94 (0.14), residues: 1314 sheet: None (None), residues: 0 loop : -1.10 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 73 HIS 0.008 0.002 HIS U 51 PHE 0.017 0.001 PHE I 25 TYR 0.026 0.003 TYR L 84 ARG 0.015 0.001 ARG K 89 ********************** 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 464 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 436 time to evaluate : 1.685 Fit side-chains REVERT: G 81 ARG cc_start: 0.7556 (mmt180) cc_final: 0.6907 (mtp180) REVERT: G 90 ASP cc_start: 0.7919 (t0) cc_final: 0.7477 (t0) REVERT: H 90 ASP cc_start: 0.7897 (t0) cc_final: 0.7433 (t0) REVERT: I 90 ASP cc_start: 0.7901 (t0) cc_final: 0.7471 (t0) REVERT: J 13 TYR cc_start: 0.8389 (m-10) cc_final: 0.7958 (m-10) REVERT: J 31 ASP cc_start: 0.8055 (m-30) cc_final: 0.7777 (m-30) REVERT: J 62 ASN cc_start: 0.8918 (m-40) cc_final: 0.8462 (m110) REVERT: J 70 MET cc_start: 0.8419 (ttp) cc_final: 0.8004 (ttm) REVERT: K 13 TYR cc_start: 0.8511 (m-10) cc_final: 0.7951 (m-10) REVERT: K 62 ASN cc_start: 0.8888 (m-40) cc_final: 0.8367 (m-40) REVERT: K 90 ASP cc_start: 0.7320 (t0) cc_final: 0.6908 (t0) REVERT: L 13 TYR cc_start: 0.8548 (m-10) cc_final: 0.8054 (m-10) REVERT: L 62 ASN cc_start: 0.8838 (m-40) cc_final: 0.8487 (m-40) REVERT: N 31 ASP cc_start: 0.8176 (m-30) cc_final: 0.7850 (m-30) REVERT: N 90 ASP cc_start: 0.7744 (t0) cc_final: 0.7389 (t0) REVERT: O 90 ASP cc_start: 0.8028 (t0) cc_final: 0.7481 (t0) REVERT: P 47 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7040 (tm-30) REVERT: P 90 ASP cc_start: 0.7785 (t0) cc_final: 0.7408 (t0) REVERT: Q 62 ASN cc_start: 0.8815 (m-40) cc_final: 0.8487 (m-40) REVERT: Q 90 ASP cc_start: 0.8057 (t0) cc_final: 0.7592 (t0) REVERT: R 62 ASN cc_start: 0.8726 (m-40) cc_final: 0.8068 (m110) REVERT: R 90 ASP cc_start: 0.7764 (t0) cc_final: 0.7351 (t0) REVERT: S 85 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6555 (mt-10) REVERT: S 90 ASP cc_start: 0.8206 (t0) cc_final: 0.7900 (t0) REVERT: T 30 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7587 (mt-10) REVERT: T 47 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6912 (mm-30) REVERT: U 62 ASN cc_start: 0.9028 (m110) cc_final: 0.8602 (m110) REVERT: U 90 ASP cc_start: 0.7862 (t0) cc_final: 0.7647 (t0) REVERT: V 27 MET cc_start: 0.8526 (ttp) cc_final: 0.8319 (ttt) REVERT: V 36 LYS cc_start: 0.7707 (mttt) cc_final: 0.7329 (mtpt) REVERT: W 12 ARG cc_start: 0.7621 (mmm160) cc_final: 0.7367 (tpt90) REVERT: W 36 LYS cc_start: 0.7599 (mtpt) cc_final: 0.7258 (mtpt) REVERT: X 15 GLU cc_start: 0.7703 (tt0) cc_final: 0.7483 (tt0) REVERT: X 91 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 28 outliers final: 22 residues processed: 451 average time/residue: 0.3297 time to fit residues: 200.4100 Evaluate side-chains 456 residues out of total 1422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 433 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain M residue 56 THR 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 P residue 47 GLU Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 27 MET 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 10 LEU 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 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111172 restraints weight = 17630.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115100 restraints weight = 10097.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117805 restraints weight = 6607.933| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4620 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= 0.192 Angle : 0.590 8.767 18810 Z= 0.319 Chirality : 0.035 0.201 1944 Planarity : 0.006 0.062 2412 Dihedral : 3.971 15.438 1800 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.13 % Allowed : 26.58 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1620 helix: 0.92 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -1.00 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP M 94 HIS 0.009 0.001 HIS G 51 PHE 0.015 0.001 PHE I 25 TYR 0.025 0.002 TYR L 84 ARG 0.014 0.001 ARG J 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3560.88 seconds wall clock time: 63 minutes 29.39 seconds (3809.39 seconds total)