Starting phenix.real_space_refine on Sat May 10 20:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.map" model { file = "/net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adv_15371/05_2025/8adv_15371.cif" } resolution = 2.98 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4320 2.51 5 N 1200 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.10, per 1000 atoms: 0.30 Number of scatterers: 6920 At special positions: 0 Unit cell: (120.75, 129.15, 51.45, 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 20 16.00 O 1380 8.00 N 1200 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 987.0 milliseconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.280A pdb=" N VAL A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA C 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU E 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL E 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA G 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA E 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU G 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL G 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA I 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS C 34 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 35 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 34 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 35 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS G 34 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 35 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS I 34 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 35 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 58 removed outlier: 9.280A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AB2, first strand: chain 'A' and resid 82 through 83 removed outlier: 5.969A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL C 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL E 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL G 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY C 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS E 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS G 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY G 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS I 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL G 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.279A pdb=" N VAL B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA D 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU D 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA F 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA D 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU F 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA H 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA F 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU H 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL H 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA J 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA H 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU J 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA H 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS D 34 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 35 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 34 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 35 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS H 34 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU F 35 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS J 34 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 35 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 58 removed outlier: 9.279A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL F 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL H 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY F 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR H 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS J 58 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU H 57 " --> pdb=" O LYS J 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 79 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.968A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL D 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL F 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL H 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS J 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 144 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.92 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: 2290 1.34 - 1.45: 656 1.45 - 1.57: 3964 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 6950 Sorted by residual: bond pdb=" CG LEU E 38 " pdb=" CD1 LEU E 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU G 38 " pdb=" CD1 LEU G 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 8612 1.00 - 2.00: 543 2.00 - 2.99: 95 2.99 - 3.99: 57 3.99 - 4.99: 13 Bond angle restraints: 9320 Sorted by residual: angle pdb=" C VAL J 3 " pdb=" N PHE J 4 " pdb=" CA PHE J 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 6.00e+00 angle pdb=" C VAL C 3 " pdb=" N PHE C 4 " pdb=" CA PHE C 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 6.00e+00 angle pdb=" C VAL D 3 " pdb=" N PHE D 4 " pdb=" CA PHE D 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 5.99e+00 angle pdb=" C VAL E 3 " pdb=" N PHE E 4 " pdb=" CA PHE E 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 5.99e+00 angle pdb=" C VAL B 3 " pdb=" N PHE B 4 " pdb=" CA PHE B 4 " ideal model delta sigma weight residual 122.53 118.60 3.93 1.61e+00 3.86e-01 5.97e+00 ... (remaining 9315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 3880 15.24 - 30.48: 190 30.48 - 45.72: 70 45.72 - 60.96: 30 60.96 - 76.20: 10 Dihedral angle restraints: 4180 sinusoidal: 1490 harmonic: 2690 Sorted by residual: dihedral pdb=" CA ALA B 85 " pdb=" C ALA B 85 " pdb=" N GLY B 86 " pdb=" CA GLY B 86 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ALA E 85 " pdb=" C ALA E 85 " pdb=" N GLY E 86 " pdb=" CA GLY E 86 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ALA J 85 " pdb=" C ALA J 85 " pdb=" N GLY J 86 " pdb=" CA GLY J 86 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 578 0.033 - 0.066: 339 0.066 - 0.099: 168 0.099 - 0.132: 65 0.132 - 0.165: 10 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB VAL C 37 " pdb=" CA VAL C 37 " pdb=" CG1 VAL C 37 " pdb=" CG2 VAL C 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB VAL B 37 " pdb=" CA VAL B 37 " pdb=" CG1 VAL B 37 " pdb=" CG2 VAL B 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB VAL F 37 " pdb=" CA VAL F 37 " pdb=" CG1 VAL F 37 " pdb=" CG2 VAL F 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 1157 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 4 " -0.011 2.00e-02 2.50e+03 8.78e-03 1.35e+00 pdb=" CG PHE G 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE G 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 4 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.011 2.00e-02 2.50e+03 8.71e-03 1.33e+00 pdb=" CG PHE A 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 4 " 0.011 2.00e-02 2.50e+03 8.64e-03 1.31e+00 pdb=" CG PHE F 4 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE F 4 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 4 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 4 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 184 2.68 - 3.24: 6273 3.24 - 3.79: 10911 3.79 - 4.35: 15601 4.35 - 4.90: 27802 Nonbonded interactions: 60771 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU C 46 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR E 39 " pdb=" OE2 GLU E 46 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR F 39 " pdb=" OE2 GLU F 46 " model vdw 2.127 3.040 nonbonded pdb=" OH TYR I 39 " pdb=" OE2 GLU I 46 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR D 39 " pdb=" OE2 GLU D 46 " model vdw 2.128 3.040 ... (remaining 60766 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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 individual isotropic 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.064 6950 Z= 0.273 Angle : 0.636 4.991 9320 Z= 0.365 Chirality : 0.053 0.165 1160 Planarity : 0.002 0.009 1170 Dihedral : 12.650 76.203 2480 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.45 % Allowed : 0.00 % Favored : 98.55 % 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: -3.72 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 PHE 0.020 0.005 PHE G 4 TYR 0.015 0.004 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.11793 ( 144) hydrogen bonds : angle 8.13050 ( 432) covalent geometry : bond 0.00574 ( 6950) covalent geometry : angle 0.63587 ( 9320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.714 Fit side-chains REVERT: A 5 MET cc_start: 0.7766 (ttm) cc_final: 0.7468 (ttm) REVERT: B 65 ASN cc_start: 0.8795 (m110) cc_final: 0.8525 (m110) REVERT: C 61 GLU cc_start: 0.7573 (mp0) cc_final: 0.7114 (mp0) REVERT: E 5 MET cc_start: 0.7884 (ttm) cc_final: 0.7680 (ttm) REVERT: E 65 ASN cc_start: 0.8599 (m110) cc_final: 0.8387 (m-40) REVERT: G 61 GLU cc_start: 0.7429 (mp0) cc_final: 0.7210 (mp0) REVERT: I 2 ASP cc_start: 0.8041 (m-30) cc_final: 0.7718 (m-30) REVERT: I 65 ASN cc_start: 0.8531 (m110) cc_final: 0.8251 (m-40) REVERT: J 65 ASN cc_start: 0.8568 (m110) cc_final: 0.8077 (m110) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 1.1499 time to fit residues: 189.8862 Evaluate side-chains 149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092974 restraints weight = 8518.124| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.27 r_work: 0.3204 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6950 Z= 0.224 Angle : 0.580 5.859 9320 Z= 0.320 Chirality : 0.051 0.128 1160 Planarity : 0.002 0.015 1170 Dihedral : 5.309 17.394 990 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.90 % Allowed : 12.46 % Favored : 84.64 % 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: -3.67 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE C 4 TYR 0.018 0.004 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.02863 ( 144) hydrogen bonds : angle 5.96673 ( 432) covalent geometry : bond 0.00488 ( 6950) covalent geometry : angle 0.57968 ( 9320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.701 Fit side-chains REVERT: A 5 MET cc_start: 0.8209 (ttm) cc_final: 0.7900 (ttm) REVERT: A 46 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8519 (mt-10) REVERT: B 65 ASN cc_start: 0.9010 (m110) cc_final: 0.8762 (m110) REVERT: C 46 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 61 GLU cc_start: 0.8213 (mp0) cc_final: 0.7561 (mp0) REVERT: E 61 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: F 61 GLU cc_start: 0.8402 (mp0) cc_final: 0.8099 (mp0) REVERT: G 61 GLU cc_start: 0.7984 (mp0) cc_final: 0.7620 (mp0) REVERT: H 61 GLU cc_start: 0.8190 (mp0) cc_final: 0.7801 (mp0) REVERT: I 20 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: I 65 ASN cc_start: 0.8800 (m110) cc_final: 0.8522 (m-40) REVERT: J 65 ASN cc_start: 0.8764 (m110) cc_final: 0.8311 (m110) outliers start: 20 outliers final: 7 residues processed: 171 average time/residue: 1.1550 time to fit residues: 207.8615 Evaluate side-chains 174 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091908 restraints weight = 9424.488| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.37 r_work: 0.3228 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 6950 Z= 0.294 Angle : 0.615 6.641 9320 Z= 0.339 Chirality : 0.053 0.129 1160 Planarity : 0.002 0.013 1170 Dihedral : 5.453 19.497 990 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.51 % Allowed : 14.78 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.018 0.004 PHE C 4 TYR 0.022 0.005 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 144) hydrogen bonds : angle 5.83296 ( 432) covalent geometry : bond 0.00642 ( 6950) covalent geometry : angle 0.61480 ( 9320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.765 Fit side-chains REVERT: A 5 MET cc_start: 0.8307 (ttm) cc_final: 0.8014 (ttm) REVERT: A 20 GLU cc_start: 0.8591 (tt0) cc_final: 0.8129 (tt0) REVERT: C 2 ASP cc_start: 0.8173 (m-30) cc_final: 0.7791 (m-30) REVERT: C 61 GLU cc_start: 0.8140 (mp0) cc_final: 0.7563 (mp0) REVERT: D 2 ASP cc_start: 0.8518 (m-30) cc_final: 0.8172 (m-30) REVERT: D 20 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: D 99 GLN cc_start: 0.6596 (mt0) cc_final: 0.6389 (mt0) REVERT: E 61 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: F 61 GLU cc_start: 0.8434 (mp0) cc_final: 0.8078 (mp0) REVERT: G 61 GLU cc_start: 0.8008 (mp0) cc_final: 0.7679 (mp0) REVERT: H 2 ASP cc_start: 0.8361 (m-30) cc_final: 0.7766 (m-30) REVERT: H 61 GLU cc_start: 0.8208 (mp0) cc_final: 0.7371 (mp0) REVERT: I 61 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: I 65 ASN cc_start: 0.8755 (m110) cc_final: 0.8478 (m-40) REVERT: J 2 ASP cc_start: 0.8385 (m-30) cc_final: 0.8112 (m-30) REVERT: J 65 ASN cc_start: 0.8775 (m110) cc_final: 0.8331 (m110) outliers start: 38 outliers final: 21 residues processed: 180 average time/residue: 1.1528 time to fit residues: 218.1585 Evaluate side-chains 186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.106877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091691 restraints weight = 9461.988| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.38 r_work: 0.3227 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 6950 Z= 0.301 Angle : 0.610 6.317 9320 Z= 0.337 Chirality : 0.053 0.127 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.515 20.290 990 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.78 % Allowed : 18.12 % Favored : 77.10 % 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: -3.59 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.019 0.004 PHE C 4 TYR 0.020 0.005 TYR G 39 Details of bonding type rmsd hydrogen bonds : bond 0.02531 ( 144) hydrogen bonds : angle 5.73407 ( 432) covalent geometry : bond 0.00657 ( 6950) covalent geometry : angle 0.61031 ( 9320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.770 Fit side-chains REVERT: A 5 MET cc_start: 0.8278 (ttm) cc_final: 0.7964 (ttm) REVERT: A 20 GLU cc_start: 0.8606 (tt0) cc_final: 0.8146 (tt0) REVERT: A 65 ASN cc_start: 0.9168 (m110) cc_final: 0.8871 (m110) REVERT: B 2 ASP cc_start: 0.8314 (m-30) cc_final: 0.7864 (m-30) REVERT: C 2 ASP cc_start: 0.8047 (m-30) cc_final: 0.7683 (m-30) REVERT: C 61 GLU cc_start: 0.8204 (mp0) cc_final: 0.7670 (mp0) REVERT: D 2 ASP cc_start: 0.8499 (m-30) cc_final: 0.8099 (m-30) REVERT: D 20 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: F 61 GLU cc_start: 0.8473 (mp0) cc_final: 0.8077 (mp0) REVERT: G 1 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.5953 (tmm) REVERT: G 61 GLU cc_start: 0.8095 (mp0) cc_final: 0.7678 (mp0) REVERT: H 2 ASP cc_start: 0.8388 (m-30) cc_final: 0.7811 (m-30) REVERT: H 61 GLU cc_start: 0.8231 (mp0) cc_final: 0.7369 (mp0) REVERT: I 2 ASP cc_start: 0.8471 (m-30) cc_final: 0.8030 (m-30) REVERT: I 61 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: I 65 ASN cc_start: 0.8721 (m110) cc_final: 0.8456 (m-40) REVERT: J 2 ASP cc_start: 0.8401 (m-30) cc_final: 0.8128 (m-30) REVERT: J 61 GLU cc_start: 0.8505 (mp0) cc_final: 0.8151 (mp0) REVERT: J 65 ASN cc_start: 0.8795 (m110) cc_final: 0.8334 (m110) outliers start: 33 outliers final: 23 residues processed: 173 average time/residue: 1.1406 time to fit residues: 207.7196 Evaluate side-chains 184 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096365 restraints weight = 8630.475| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.26 r_work: 0.3277 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6950 Z= 0.127 Angle : 0.507 7.125 9320 Z= 0.277 Chirality : 0.050 0.121 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.027 16.337 990 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.20 % Allowed : 19.28 % Favored : 76.52 % 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: -3.58 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.014 0.003 PHE D 4 TYR 0.009 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01945 ( 144) hydrogen bonds : angle 5.47248 ( 432) covalent geometry : bond 0.00272 ( 6950) covalent geometry : angle 0.50697 ( 9320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.923 Fit side-chains REVERT: A 5 MET cc_start: 0.8141 (ttm) cc_final: 0.7855 (ttm) REVERT: A 65 ASN cc_start: 0.9135 (m110) cc_final: 0.8858 (m110) REVERT: B 5 MET cc_start: 0.7950 (ttm) cc_final: 0.7634 (ttm) REVERT: B 61 GLU cc_start: 0.8482 (mp0) cc_final: 0.8277 (mp0) REVERT: C 2 ASP cc_start: 0.7948 (m-30) cc_final: 0.7620 (m-30) REVERT: C 61 GLU cc_start: 0.8238 (mp0) cc_final: 0.7787 (mp0) REVERT: D 2 ASP cc_start: 0.8402 (m-30) cc_final: 0.8042 (m-30) REVERT: D 20 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: D 61 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8033 (mp0) REVERT: E 61 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: F 61 GLU cc_start: 0.8422 (mp0) cc_final: 0.8029 (mp0) REVERT: G 1 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.5971 (tmm) REVERT: G 35 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: G 61 GLU cc_start: 0.8036 (mp0) cc_final: 0.7515 (mp0) REVERT: H 61 GLU cc_start: 0.8208 (mp0) cc_final: 0.7278 (mp0) REVERT: I 65 ASN cc_start: 0.8727 (m110) cc_final: 0.8479 (m-40) REVERT: J 61 GLU cc_start: 0.8411 (mp0) cc_final: 0.8114 (mp0) REVERT: J 65 ASN cc_start: 0.8770 (m110) cc_final: 0.8273 (m110) outliers start: 29 outliers final: 14 residues processed: 177 average time/residue: 1.1469 time to fit residues: 214.0584 Evaluate side-chains 175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.102481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087464 restraints weight = 10096.283| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.50 r_work: 0.3172 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6950 Z= 0.272 Angle : 0.583 8.042 9320 Z= 0.320 Chirality : 0.052 0.126 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.278 19.516 990 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.93 % Allowed : 20.72 % Favored : 74.35 % 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: -3.51 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.016 0.004 PHE A 4 TYR 0.018 0.004 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02203 ( 144) hydrogen bonds : angle 5.49723 ( 432) covalent geometry : bond 0.00592 ( 6950) covalent geometry : angle 0.58298 ( 9320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.753 Fit side-chains REVERT: A 5 MET cc_start: 0.8314 (ttm) cc_final: 0.8014 (ttm) REVERT: A 20 GLU cc_start: 0.8519 (tt0) cc_final: 0.8031 (tt0) REVERT: A 65 ASN cc_start: 0.9159 (m110) cc_final: 0.8864 (m110) REVERT: B 5 MET cc_start: 0.8458 (ttm) cc_final: 0.8140 (ttm) REVERT: C 2 ASP cc_start: 0.8052 (m-30) cc_final: 0.7695 (m-30) REVERT: C 61 GLU cc_start: 0.8111 (mp0) cc_final: 0.7636 (mp0) REVERT: D 2 ASP cc_start: 0.8594 (m-30) cc_final: 0.8190 (m-30) REVERT: D 20 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: E 61 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: F 61 GLU cc_start: 0.8417 (mp0) cc_final: 0.8001 (mp0) REVERT: G 1 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.5913 (tmm) REVERT: G 35 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: G 61 GLU cc_start: 0.8024 (mp0) cc_final: 0.7412 (mp0) REVERT: H 2 ASP cc_start: 0.8482 (m-30) cc_final: 0.7907 (m-30) REVERT: H 61 GLU cc_start: 0.8194 (mp0) cc_final: 0.7325 (mp0) REVERT: I 2 ASP cc_start: 0.8334 (m-30) cc_final: 0.7915 (m-30) REVERT: I 65 ASN cc_start: 0.8697 (m110) cc_final: 0.8448 (m-40) REVERT: J 2 ASP cc_start: 0.8372 (m-30) cc_final: 0.8066 (m-30) REVERT: J 61 GLU cc_start: 0.8386 (mp0) cc_final: 0.8103 (mp0) REVERT: J 65 ASN cc_start: 0.8713 (m110) cc_final: 0.8188 (m110) outliers start: 34 outliers final: 19 residues processed: 179 average time/residue: 1.1756 time to fit residues: 221.5229 Evaluate side-chains 186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093695 restraints weight = 9234.566| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.35 r_work: 0.3266 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 6950 Z= 0.224 Angle : 0.561 8.571 9320 Z= 0.307 Chirality : 0.051 0.125 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.243 18.740 990 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.22 % Allowed : 21.16 % Favored : 73.62 % 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: -3.50 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE D 4 TYR 0.015 0.004 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02099 ( 144) hydrogen bonds : angle 5.44408 ( 432) covalent geometry : bond 0.00488 ( 6950) covalent geometry : angle 0.56100 ( 9320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.813 Fit side-chains REVERT: A 5 MET cc_start: 0.8249 (ttm) cc_final: 0.7958 (ttm) REVERT: A 20 GLU cc_start: 0.8520 (tt0) cc_final: 0.8008 (tt0) REVERT: A 65 ASN cc_start: 0.9142 (m110) cc_final: 0.8851 (m110) REVERT: B 5 MET cc_start: 0.8406 (ttm) cc_final: 0.8089 (ttm) REVERT: C 2 ASP cc_start: 0.7942 (m-30) cc_final: 0.7610 (m-30) REVERT: C 61 GLU cc_start: 0.8149 (mp0) cc_final: 0.7722 (mp0) REVERT: D 2 ASP cc_start: 0.8541 (m-30) cc_final: 0.8127 (m-30) REVERT: D 20 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: E 2 ASP cc_start: 0.8578 (m-30) cc_final: 0.8354 (m-30) REVERT: E 61 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: F 5 MET cc_start: 0.8581 (ttm) cc_final: 0.8242 (ttm) REVERT: F 61 GLU cc_start: 0.8469 (mp0) cc_final: 0.8091 (mp0) REVERT: G 1 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.5890 (tmm) REVERT: G 20 GLU cc_start: 0.8773 (tt0) cc_final: 0.8509 (tt0) REVERT: G 35 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: G 61 GLU cc_start: 0.8059 (mp0) cc_final: 0.7445 (mp0) REVERT: H 2 ASP cc_start: 0.8469 (m-30) cc_final: 0.7915 (m-30) REVERT: H 61 GLU cc_start: 0.8258 (mp0) cc_final: 0.7356 (mp0) REVERT: H 79 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: I 2 ASP cc_start: 0.8274 (m-30) cc_final: 0.7853 (m-30) REVERT: I 65 ASN cc_start: 0.8833 (m110) cc_final: 0.8587 (m-40) REVERT: J 2 ASP cc_start: 0.8364 (m-30) cc_final: 0.8078 (m-30) REVERT: J 61 GLU cc_start: 0.8418 (mp0) cc_final: 0.8106 (mp0) REVERT: J 65 ASN cc_start: 0.8800 (m110) cc_final: 0.8289 (m110) outliers start: 36 outliers final: 22 residues processed: 181 average time/residue: 1.1276 time to fit residues: 214.5953 Evaluate side-chains 189 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 0.0010 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 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 = 0.102356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087330 restraints weight = 10106.097| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.50 r_work: 0.3172 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6950 Z= 0.265 Angle : 0.591 8.810 9320 Z= 0.323 Chirality : 0.052 0.128 1160 Planarity : 0.002 0.011 1170 Dihedral : 5.344 19.744 990 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.93 % Allowed : 22.03 % Favored : 73.04 % 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: -3.50 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.017 0.004 PHE D 4 TYR 0.016 0.004 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02180 ( 144) hydrogen bonds : angle 5.46785 ( 432) covalent geometry : bond 0.00578 ( 6950) covalent geometry : angle 0.59133 ( 9320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.723 Fit side-chains REVERT: A 5 MET cc_start: 0.8266 (ttm) cc_final: 0.7964 (ttm) REVERT: A 20 GLU cc_start: 0.8512 (tt0) cc_final: 0.8017 (tt0) REVERT: A 65 ASN cc_start: 0.9144 (m110) cc_final: 0.8853 (m110) REVERT: B 5 MET cc_start: 0.8483 (ttm) cc_final: 0.8238 (ttm) REVERT: C 2 ASP cc_start: 0.8002 (m-30) cc_final: 0.7650 (m-30) REVERT: C 61 GLU cc_start: 0.8144 (mp0) cc_final: 0.7680 (mp0) REVERT: D 2 ASP cc_start: 0.8610 (m-30) cc_final: 0.8164 (m-30) REVERT: D 20 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: E 61 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: F 5 MET cc_start: 0.8605 (ttm) cc_final: 0.8270 (ttm) REVERT: F 61 GLU cc_start: 0.8437 (mp0) cc_final: 0.8040 (mp0) REVERT: G 1 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.5923 (tmm) REVERT: G 20 GLU cc_start: 0.8709 (tt0) cc_final: 0.8480 (tt0) REVERT: G 35 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: G 61 GLU cc_start: 0.8067 (mp0) cc_final: 0.7403 (mp0) REVERT: H 2 ASP cc_start: 0.8592 (m-30) cc_final: 0.8004 (m-30) REVERT: H 61 GLU cc_start: 0.8228 (mp0) cc_final: 0.7312 (mp0) REVERT: H 79 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: I 2 ASP cc_start: 0.8463 (m-30) cc_final: 0.7995 (m-30) REVERT: I 65 ASN cc_start: 0.8750 (m110) cc_final: 0.8513 (m-40) REVERT: J 2 ASP cc_start: 0.8414 (m-30) cc_final: 0.8116 (m-30) REVERT: J 61 GLU cc_start: 0.8384 (mp0) cc_final: 0.8097 (mp0) REVERT: J 65 ASN cc_start: 0.8693 (m110) cc_final: 0.8158 (m110) outliers start: 34 outliers final: 26 residues processed: 180 average time/residue: 1.0625 time to fit residues: 201.7132 Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087437 restraints weight = 10142.124| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.51 r_work: 0.3175 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6950 Z= 0.253 Angle : 0.586 8.975 9320 Z= 0.320 Chirality : 0.052 0.129 1160 Planarity : 0.002 0.019 1170 Dihedral : 5.350 19.640 990 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.36 % Allowed : 22.03 % Favored : 72.61 % 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: -3.50 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.017 0.004 PHE D 4 TYR 0.016 0.004 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02147 ( 144) hydrogen bonds : angle 5.44735 ( 432) covalent geometry : bond 0.00552 ( 6950) covalent geometry : angle 0.58629 ( 9320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.814 Fit side-chains REVERT: A 5 MET cc_start: 0.8270 (ttm) cc_final: 0.7973 (ttm) REVERT: A 20 GLU cc_start: 0.8516 (tt0) cc_final: 0.8017 (tt0) REVERT: A 65 ASN cc_start: 0.9140 (m110) cc_final: 0.8840 (m110) REVERT: B 5 MET cc_start: 0.8463 (ttm) cc_final: 0.8217 (ttm) REVERT: C 2 ASP cc_start: 0.8030 (m-30) cc_final: 0.7614 (m-30) REVERT: C 61 GLU cc_start: 0.8172 (mp0) cc_final: 0.7702 (mp0) REVERT: D 2 ASP cc_start: 0.8614 (m-30) cc_final: 0.8137 (m-30) REVERT: D 20 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: E 61 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: F 1 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6268 (tmm) REVERT: F 5 MET cc_start: 0.8597 (ttm) cc_final: 0.8251 (ttm) REVERT: F 61 GLU cc_start: 0.8437 (mp0) cc_final: 0.8026 (mp0) REVERT: G 1 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.5861 (tmm) REVERT: G 20 GLU cc_start: 0.8697 (tt0) cc_final: 0.8437 (tt0) REVERT: G 35 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7962 (tp30) REVERT: G 61 GLU cc_start: 0.8001 (mp0) cc_final: 0.7338 (mp0) REVERT: H 2 ASP cc_start: 0.8489 (m-30) cc_final: 0.7898 (m-30) REVERT: H 61 GLU cc_start: 0.8236 (mp0) cc_final: 0.7271 (mp0) REVERT: H 79 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: I 2 ASP cc_start: 0.8334 (m-30) cc_final: 0.7896 (m-30) REVERT: I 65 ASN cc_start: 0.8745 (m110) cc_final: 0.8496 (m-40) REVERT: I 79 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: J 2 ASP cc_start: 0.8416 (m-30) cc_final: 0.8109 (m-30) REVERT: J 61 GLU cc_start: 0.8395 (mp0) cc_final: 0.8078 (mp0) REVERT: J 65 ASN cc_start: 0.8688 (m110) cc_final: 0.8149 (m110) outliers start: 37 outliers final: 29 residues processed: 183 average time/residue: 1.0950 time to fit residues: 211.1897 Evaluate side-chains 200 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088411 restraints weight = 10197.745| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.52 r_work: 0.3190 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6950 Z= 0.213 Angle : 0.568 9.096 9320 Z= 0.309 Chirality : 0.051 0.129 1160 Planarity : 0.002 0.013 1170 Dihedral : 5.264 18.698 990 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.20 % Allowed : 22.90 % Favored : 72.90 % 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: -3.50 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE D 4 TYR 0.014 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02041 ( 144) hydrogen bonds : angle 5.39951 ( 432) covalent geometry : bond 0.00464 ( 6950) covalent geometry : angle 0.56768 ( 9320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.708 Fit side-chains REVERT: A 5 MET cc_start: 0.8257 (ttm) cc_final: 0.7961 (ttm) REVERT: A 20 GLU cc_start: 0.8487 (tt0) cc_final: 0.7994 (tt0) REVERT: A 65 ASN cc_start: 0.9127 (m110) cc_final: 0.8829 (m110) REVERT: B 5 MET cc_start: 0.8424 (ttm) cc_final: 0.8116 (ttm) REVERT: C 2 ASP cc_start: 0.7978 (m-30) cc_final: 0.7577 (m-30) REVERT: C 61 GLU cc_start: 0.8212 (mp0) cc_final: 0.7723 (mp0) REVERT: D 2 ASP cc_start: 0.8599 (m-30) cc_final: 0.8112 (m-30) REVERT: D 20 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: E 61 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: F 5 MET cc_start: 0.8573 (ttm) cc_final: 0.8228 (ttm) REVERT: F 61 GLU cc_start: 0.8421 (mp0) cc_final: 0.8012 (mp0) REVERT: G 1 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.5765 (tmm) REVERT: G 20 GLU cc_start: 0.8678 (tt0) cc_final: 0.8407 (tt0) REVERT: G 35 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: G 61 GLU cc_start: 0.7993 (mp0) cc_final: 0.7338 (mp0) REVERT: H 2 ASP cc_start: 0.8472 (m-30) cc_final: 0.7871 (m-30) REVERT: H 61 GLU cc_start: 0.8229 (mp0) cc_final: 0.7285 (mp0) REVERT: H 79 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: I 2 ASP cc_start: 0.8264 (m-30) cc_final: 0.7817 (m-30) REVERT: I 65 ASN cc_start: 0.8717 (m110) cc_final: 0.8480 (m-40) REVERT: I 79 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: J 2 ASP cc_start: 0.8395 (m-30) cc_final: 0.8095 (m-30) REVERT: J 61 GLU cc_start: 0.8386 (mp0) cc_final: 0.8067 (mp0) REVERT: J 65 ASN cc_start: 0.8698 (m110) cc_final: 0.8136 (m110) outliers start: 29 outliers final: 23 residues processed: 180 average time/residue: 1.1218 time to fit residues: 212.7268 Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain J residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087895 restraints weight = 10107.816| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.50 r_work: 0.3184 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6950 Z= 0.238 Angle : 0.584 9.393 9320 Z= 0.317 Chirality : 0.051 0.129 1160 Planarity : 0.002 0.018 1170 Dihedral : 5.311 19.243 990 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.06 % Allowed : 23.04 % Favored : 72.90 % 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: -3.50 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.017 0.004 PHE D 4 TYR 0.016 0.004 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02097 ( 144) hydrogen bonds : angle 5.41530 ( 432) covalent geometry : bond 0.00518 ( 6950) covalent geometry : angle 0.58425 ( 9320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5014.94 seconds wall clock time: 88 minutes 1.61 seconds (5281.61 seconds total)