Starting phenix.real_space_refine on Fri Aug 22 18:28:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adv_15371/08_2025/8adv_15371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adv_15371/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8adv_15371/08_2025/8adv_15371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adv_15371/08_2025/8adv_15371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8adv_15371/08_2025/8adv_15371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adv_15371/08_2025/8adv_15371.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.66, per 1000 atoms: 0.10 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: 0.39 Conformation dependent library (CDL) restraints added in 276.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.23 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: 0.84 Time building geometry restraints manager: 0.55 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.960 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- 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 : 16.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.015 0.004 TYR H 39 PHE 0.020 0.005 PHE G 4 HIS 0.001 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 6950) covalent geometry : angle 0.63587 ( 9320) hydrogen bonds : bond 0.11793 ( 144) hydrogen bonds : angle 8.13050 ( 432) *********************** 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 : 0.256 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: 0.7211 (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: 0.8250 (m-40) REVERT: J 65 ASN cc_start: 0.8568 (m110) cc_final: 0.8078 (m110) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 0.5757 time to fit residues: 94.6992 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 : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.109463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093847 restraints weight = 8639.527| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.26 r_work: 0.3215 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6950 Z= 0.193 Angle : 0.560 5.615 9320 Z= 0.309 Chirality : 0.050 0.124 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.221 16.708 990 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.75 % Allowed : 12.17 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (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 TYR 0.015 0.003 TYR C 39 PHE 0.017 0.004 PHE H 4 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 6950) covalent geometry : angle 0.55999 ( 9320) hydrogen bonds : bond 0.02955 ( 144) hydrogen bonds : angle 5.98837 ( 432) *********************** 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 185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.291 Fit side-chains REVERT: A 2 ASP cc_start: 0.8270 (m-30) cc_final: 0.8037 (m-30) REVERT: A 5 MET cc_start: 0.8179 (ttm) cc_final: 0.7869 (ttm) REVERT: A 46 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8454 (mt-10) REVERT: B 5 MET cc_start: 0.8199 (ttm) cc_final: 0.7966 (ttm) REVERT: B 65 ASN cc_start: 0.8999 (m110) cc_final: 0.8738 (m110) REVERT: C 46 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 61 GLU cc_start: 0.8227 (mp0) cc_final: 0.7583 (mp0) REVERT: E 61 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: G 61 GLU cc_start: 0.7976 (mp0) cc_final: 0.7635 (mp0) REVERT: H 61 GLU cc_start: 0.8194 (mp0) cc_final: 0.7873 (mp0) REVERT: I 20 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: I 61 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: I 65 ASN cc_start: 0.8806 (m110) cc_final: 0.8528 (m-40) REVERT: J 65 ASN cc_start: 0.8765 (m110) cc_final: 0.8317 (m110) outliers start: 19 outliers final: 6 residues processed: 168 average time/residue: 0.5576 time to fit residues: 98.4382 Evaluate side-chains 172 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I residue 61 GLU 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 68 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 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 = 0.3566 r_free = 0.3566 target = 0.107048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091909 restraints weight = 9275.871| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.37 r_work: 0.3234 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1411 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 : 0.621 6.124 9320 Z= 0.342 Chirality : 0.053 0.129 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.446 19.147 990 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.22 % Allowed : 14.78 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.021 0.005 TYR I 39 PHE 0.018 0.005 PHE C 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 6950) covalent geometry : angle 0.62078 ( 9320) hydrogen bonds : bond 0.02759 ( 144) hydrogen bonds : angle 5.84673 ( 432) *********************** 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 204 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.278 Fit side-chains REVERT: A 2 ASP cc_start: 0.8260 (m-30) cc_final: 0.7964 (m-30) REVERT: A 5 MET cc_start: 0.8308 (ttm) cc_final: 0.8013 (ttm) REVERT: A 20 GLU cc_start: 0.8587 (tt0) cc_final: 0.8130 (tt0) REVERT: C 2 ASP cc_start: 0.8161 (m-30) cc_final: 0.7803 (m-30) REVERT: D 1 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6125 (ttt) REVERT: D 2 ASP cc_start: 0.8479 (m-30) cc_final: 0.8104 (m-30) REVERT: E 61 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: G 1 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6009 (tmm) REVERT: G 61 GLU cc_start: 0.7989 (mp0) cc_final: 0.7701 (mp0) REVERT: H 2 ASP cc_start: 0.8359 (m-30) cc_final: 0.7756 (m-30) REVERT: H 20 GLU cc_start: 0.8758 (tt0) cc_final: 0.8523 (tt0) REVERT: H 61 GLU cc_start: 0.8214 (mp0) cc_final: 0.7515 (mp0) REVERT: I 65 ASN cc_start: 0.8774 (m110) cc_final: 0.8502 (m-40) REVERT: J 2 ASP cc_start: 0.8413 (m-30) cc_final: 0.8139 (m-30) REVERT: J 65 ASN cc_start: 0.8788 (m110) cc_final: 0.8346 (m110) outliers start: 36 outliers final: 20 residues processed: 180 average time/residue: 0.5665 time to fit residues: 107.0399 Evaluate side-chains 188 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 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 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 60 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.108211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.093094 restraints weight = 9392.260| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.36 r_work: 0.3249 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1552 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= 0.255 Angle : 0.584 6.157 9320 Z= 0.322 Chirality : 0.052 0.125 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.384 18.822 990 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.35 % Allowed : 18.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (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 TYR 0.017 0.004 TYR G 39 PHE 0.017 0.004 PHE C 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 6950) covalent geometry : angle 0.58433 ( 9320) hydrogen bonds : bond 0.02430 ( 144) hydrogen bonds : angle 5.70628 ( 432) *********************** 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 196 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.265 Fit side-chains REVERT: A 2 ASP cc_start: 0.8296 (m-30) cc_final: 0.7992 (m-30) REVERT: A 5 MET cc_start: 0.8272 (ttm) cc_final: 0.7981 (ttm) REVERT: A 20 GLU cc_start: 0.8550 (tt0) cc_final: 0.8098 (tt0) REVERT: A 65 ASN cc_start: 0.9163 (m110) cc_final: 0.8875 (m110) REVERT: B 2 ASP cc_start: 0.8332 (m-30) cc_final: 0.7851 (m-30) REVERT: B 32 LYS cc_start: 0.9232 (mttt) cc_final: 0.8919 (mtpp) REVERT: C 2 ASP cc_start: 0.8167 (m-30) cc_final: 0.7797 (m-30) REVERT: C 46 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8428 (mt-10) REVERT: C 61 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: D 1 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6150 (ttt) REVERT: D 2 ASP cc_start: 0.8506 (m-30) cc_final: 0.8083 (m-30) REVERT: D 20 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: G 1 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.5955 (tmm) REVERT: G 61 GLU cc_start: 0.8085 (mp0) cc_final: 0.7741 (mp0) REVERT: H 2 ASP cc_start: 0.8368 (m-30) cc_final: 0.7794 (m-30) REVERT: H 61 GLU cc_start: 0.8226 (mp0) cc_final: 0.7542 (mp0) REVERT: I 65 ASN cc_start: 0.8730 (m110) cc_final: 0.8445 (m-40) REVERT: J 2 ASP cc_start: 0.8389 (m-30) cc_final: 0.8092 (m-30) REVERT: J 61 GLU cc_start: 0.8505 (mp0) cc_final: 0.8140 (mp0) REVERT: J 65 ASN cc_start: 0.8827 (m110) cc_final: 0.8383 (m110) outliers start: 30 outliers final: 18 residues processed: 177 average time/residue: 0.5167 time to fit residues: 96.1128 Evaluate side-chains 186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 61 GLU 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 J residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.107834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.092657 restraints weight = 9342.688| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.36 r_work: 0.3241 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 6950 Z= 0.273 Angle : 0.596 7.314 9320 Z= 0.327 Chirality : 0.052 0.126 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.419 19.751 990 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.51 % Allowed : 18.12 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.018 0.004 TYR I 39 PHE 0.017 0.004 PHE D 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 6950) covalent geometry : angle 0.59625 ( 9320) hydrogen bonds : bond 0.02407 ( 144) hydrogen bonds : angle 5.68361 ( 432) *********************** 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 200 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.280 Fit side-chains REVERT: A 2 ASP cc_start: 0.8250 (m-30) cc_final: 0.7931 (m-30) REVERT: A 5 MET cc_start: 0.8309 (ttm) cc_final: 0.8000 (ttm) REVERT: A 20 GLU cc_start: 0.8549 (tt0) cc_final: 0.8083 (tt0) REVERT: A 65 ASN cc_start: 0.9158 (m110) cc_final: 0.8860 (m110) REVERT: B 2 ASP cc_start: 0.8285 (m-30) cc_final: 0.7826 (m-30) REVERT: B 61 GLU cc_start: 0.8571 (mp0) cc_final: 0.8360 (mp0) REVERT: C 2 ASP cc_start: 0.8102 (m-30) cc_final: 0.7770 (m-30) REVERT: C 61 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: D 1 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6282 (ttt) REVERT: D 2 ASP cc_start: 0.8497 (m-30) cc_final: 0.8069 (m-30) REVERT: D 20 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: E 61 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: F 61 GLU cc_start: 0.8436 (mp0) cc_final: 0.8089 (mp0) REVERT: G 1 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.5848 (tmm) REVERT: G 35 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: G 61 GLU cc_start: 0.8059 (mp0) cc_final: 0.7486 (mp0) REVERT: H 2 ASP cc_start: 0.8374 (m-30) cc_final: 0.7803 (m-30) REVERT: H 61 GLU cc_start: 0.8215 (mp0) cc_final: 0.7417 (mp0) REVERT: I 2 ASP cc_start: 0.8460 (m-30) cc_final: 0.8016 (m-30) REVERT: I 61 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: I 65 ASN cc_start: 0.8735 (m110) cc_final: 0.8490 (m-40) REVERT: J 2 ASP cc_start: 0.8399 (m-30) cc_final: 0.8104 (m-30) REVERT: J 61 GLU cc_start: 0.8451 (mp0) cc_final: 0.8102 (mp0) REVERT: J 65 ASN cc_start: 0.8795 (m110) cc_final: 0.8277 (m110) outliers start: 38 outliers final: 24 residues processed: 177 average time/residue: 0.5188 time to fit residues: 96.4440 Evaluate side-chains 191 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 92 THR 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.103882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088695 restraints weight = 10041.234| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.51 r_work: 0.3192 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1766 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= 0.209 Angle : 0.556 8.115 9320 Z= 0.303 Chirality : 0.051 0.125 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.274 18.678 990 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.51 % Allowed : 19.71 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR G 39 PHE 0.016 0.004 PHE D 4 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6950) covalent geometry : angle 0.55559 ( 9320) hydrogen bonds : bond 0.02229 ( 144) hydrogen bonds : angle 5.59340 ( 432) *********************** 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 203 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.299 Fit side-chains REVERT: A 2 ASP cc_start: 0.8300 (m-30) cc_final: 0.7992 (m-30) REVERT: A 5 MET cc_start: 0.8323 (ttm) cc_final: 0.8015 (ttm) REVERT: A 20 GLU cc_start: 0.8508 (tt0) cc_final: 0.7986 (tt0) REVERT: A 65 ASN cc_start: 0.9155 (m110) cc_final: 0.8861 (m110) REVERT: B 2 ASP cc_start: 0.8213 (m-30) cc_final: 0.7945 (m-30) REVERT: B 5 MET cc_start: 0.8438 (ttm) cc_final: 0.8122 (ttm) REVERT: B 32 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8928 (mtpp) REVERT: B 61 GLU cc_start: 0.8541 (mp0) cc_final: 0.8309 (mp0) REVERT: C 2 ASP cc_start: 0.8054 (m-30) cc_final: 0.7694 (m-30) REVERT: C 61 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: D 1 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6145 (ttt) REVERT: D 2 ASP cc_start: 0.8557 (m-30) cc_final: 0.8158 (m-30) REVERT: D 20 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: E 61 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: F 61 GLU cc_start: 0.8376 (mp0) cc_final: 0.8012 (mp0) REVERT: G 1 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.5846 (tmm) REVERT: G 35 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: G 61 GLU cc_start: 0.7995 (mp0) cc_final: 0.7396 (mp0) REVERT: H 2 ASP cc_start: 0.8454 (m-30) cc_final: 0.7849 (m-30) REVERT: H 61 GLU cc_start: 0.8162 (mp0) cc_final: 0.7290 (mp0) REVERT: I 65 ASN cc_start: 0.8709 (m110) cc_final: 0.8452 (m-40) REVERT: J 2 ASP cc_start: 0.8376 (m-30) cc_final: 0.8066 (m-30) REVERT: J 61 GLU cc_start: 0.8414 (mp0) cc_final: 0.8113 (mp0) REVERT: J 65 ASN cc_start: 0.8698 (m110) cc_final: 0.8161 (m110) outliers start: 38 outliers final: 21 residues processed: 182 average time/residue: 0.5687 time to fit residues: 108.6578 Evaluate side-chains 191 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 61 GLU 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091693 restraints weight = 9466.234| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.36 r_work: 0.3223 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 6950 Z= 0.312 Angle : 0.620 8.729 9320 Z= 0.339 Chirality : 0.053 0.128 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.494 20.802 990 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 : 6.09 % Allowed : 19.42 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR G 39 PHE 0.019 0.004 PHE A 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 6950) covalent geometry : angle 0.62038 ( 9320) hydrogen bonds : bond 0.02390 ( 144) hydrogen bonds : angle 5.66132 ( 432) *********************** 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 203 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.285 Fit side-chains REVERT: A 2 ASP cc_start: 0.8309 (m-30) cc_final: 0.8028 (m-30) REVERT: A 5 MET cc_start: 0.8247 (ttm) cc_final: 0.7948 (ttm) REVERT: A 20 GLU cc_start: 0.8586 (tt0) cc_final: 0.8129 (tt0) REVERT: A 65 ASN cc_start: 0.9162 (m110) cc_final: 0.8865 (m110) REVERT: B 2 ASP cc_start: 0.7906 (m-30) cc_final: 0.7676 (m-30) REVERT: B 61 GLU cc_start: 0.8538 (mp0) cc_final: 0.8335 (mp0) REVERT: C 2 ASP cc_start: 0.7968 (m-30) cc_final: 0.7598 (m-30) REVERT: C 61 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: D 2 ASP cc_start: 0.8508 (m-30) cc_final: 0.8195 (m-30) REVERT: D 20 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: D 79 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: E 61 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: F 5 MET cc_start: 0.8636 (ttm) cc_final: 0.8312 (ttm) REVERT: F 61 GLU cc_start: 0.8471 (mp0) cc_final: 0.8130 (mp0) REVERT: G 1 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.5952 (tmm) REVERT: G 35 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: G 61 GLU cc_start: 0.8084 (mp0) cc_final: 0.7461 (mp0) REVERT: H 2 ASP cc_start: 0.8457 (m-30) cc_final: 0.7903 (m-30) REVERT: H 61 GLU cc_start: 0.8211 (mp0) cc_final: 0.7407 (mp0) REVERT: I 2 ASP cc_start: 0.8466 (m-30) cc_final: 0.8019 (m-30) REVERT: I 65 ASN cc_start: 0.8833 (m110) cc_final: 0.8592 (m-40) REVERT: J 2 ASP cc_start: 0.8426 (m-30) cc_final: 0.8135 (m-30) REVERT: J 61 GLU cc_start: 0.8389 (mp0) cc_final: 0.8112 (mp0) REVERT: J 65 ASN cc_start: 0.8784 (m110) cc_final: 0.8263 (m110) outliers start: 42 outliers final: 27 residues processed: 181 average time/residue: 0.5897 time to fit residues: 111.9842 Evaluate side-chains 194 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 61 GLU 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 57 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN 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 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 I residue 22 THR 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 72 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.108426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093399 restraints weight = 9505.539| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.37 r_work: 0.3251 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6950 Z= 0.247 Angle : 0.586 8.786 9320 Z= 0.318 Chirality : 0.052 0.127 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.400 19.750 990 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.22 % Allowed : 20.87 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.004 TYR D 39 PHE 0.017 0.004 PHE H 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 6950) covalent geometry : angle 0.58589 ( 9320) hydrogen bonds : bond 0.02238 ( 144) hydrogen bonds : angle 5.59202 ( 432) *********************** 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 197 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.282 Fit side-chains REVERT: A 2 ASP cc_start: 0.8295 (m-30) cc_final: 0.7970 (m-30) REVERT: A 5 MET cc_start: 0.8209 (ttm) cc_final: 0.7919 (ttm) REVERT: A 20 GLU cc_start: 0.8541 (tt0) cc_final: 0.8079 (tt0) REVERT: A 65 ASN cc_start: 0.9144 (m110) cc_final: 0.8849 (m110) REVERT: B 5 MET cc_start: 0.8413 (ttm) cc_final: 0.8165 (ttm) REVERT: C 2 ASP cc_start: 0.7976 (m-30) cc_final: 0.7569 (m-30) REVERT: C 61 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: D 2 ASP cc_start: 0.8497 (m-30) cc_final: 0.8181 (m-30) REVERT: D 20 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: E 61 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: F 61 GLU cc_start: 0.8496 (mp0) cc_final: 0.8118 (mp0) REVERT: G 1 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.5860 (tmm) REVERT: G 35 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: G 61 GLU cc_start: 0.8027 (mp0) cc_final: 0.7407 (mp0) REVERT: H 2 ASP cc_start: 0.8485 (m-30) cc_final: 0.7908 (m-30) REVERT: H 61 GLU cc_start: 0.8222 (mp0) cc_final: 0.7370 (mp0) REVERT: I 2 ASP cc_start: 0.8445 (m-30) cc_final: 0.8006 (m-30) REVERT: I 65 ASN cc_start: 0.8823 (m110) cc_final: 0.8582 (m-40) REVERT: I 79 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: J 2 ASP cc_start: 0.8411 (m-30) cc_final: 0.8114 (m-30) REVERT: J 61 GLU cc_start: 0.8417 (mp0) cc_final: 0.8125 (mp0) REVERT: J 65 ASN cc_start: 0.8802 (m110) cc_final: 0.8258 (m110) outliers start: 36 outliers final: 26 residues processed: 180 average time/residue: 0.5898 time to fit residues: 111.6056 Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 61 GLU 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 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 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 I residue 22 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 61 optimal weight: 0.0370 chunk 75 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 0.0020 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3546 r_free = 0.3546 target = 0.104257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089174 restraints weight = 10088.209| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.49 r_work: 0.3205 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6950 Z= 0.194 Angle : 0.562 8.700 9320 Z= 0.304 Chirality : 0.051 0.125 1160 Planarity : 0.002 0.011 1170 Dihedral : 5.259 18.362 990 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.20 % Allowed : 22.46 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (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 TYR 0.013 0.003 TYR D 39 PHE 0.016 0.003 PHE H 4 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6950) covalent geometry : angle 0.56213 ( 9320) hydrogen bonds : bond 0.02074 ( 144) hydrogen bonds : angle 5.50614 ( 432) *********************** 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 195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.318 Fit side-chains REVERT: A 2 ASP cc_start: 0.8323 (m-30) cc_final: 0.7980 (m-30) REVERT: A 5 MET cc_start: 0.8220 (ttm) cc_final: 0.7922 (ttm) REVERT: A 20 GLU cc_start: 0.8506 (tt0) cc_final: 0.8021 (tt0) REVERT: A 65 ASN cc_start: 0.9141 (m110) cc_final: 0.8837 (m110) REVERT: A 98 ASP cc_start: 0.8468 (m-30) cc_final: 0.8246 (m-30) REVERT: B 5 MET cc_start: 0.8251 (ttm) cc_final: 0.7952 (ttm) REVERT: C 2 ASP cc_start: 0.8029 (m-30) cc_final: 0.7599 (m-30) REVERT: C 61 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: D 1 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6011 (ttt) REVERT: D 2 ASP cc_start: 0.8573 (m-30) cc_final: 0.8231 (m-30) REVERT: E 61 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: F 61 GLU cc_start: 0.8426 (mp0) cc_final: 0.8029 (mp0) REVERT: G 1 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.5934 (tmm) REVERT: G 35 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: G 61 GLU cc_start: 0.7929 (mp0) cc_final: 0.7335 (mp0) REVERT: H 2 ASP cc_start: 0.8453 (m-30) cc_final: 0.7836 (m-30) REVERT: H 61 GLU cc_start: 0.8182 (mp0) cc_final: 0.7291 (mp0) REVERT: I 2 ASP cc_start: 0.8204 (m-30) cc_final: 0.7786 (m-30) REVERT: I 65 ASN cc_start: 0.8746 (m110) cc_final: 0.8499 (m-40) REVERT: J 2 ASP cc_start: 0.8391 (m-30) cc_final: 0.8096 (m-30) REVERT: J 61 GLU cc_start: 0.8399 (mp0) cc_final: 0.8090 (mp0) REVERT: J 65 ASN cc_start: 0.8699 (m110) cc_final: 0.8130 (m110) outliers start: 29 outliers final: 22 residues processed: 183 average time/residue: 0.5829 time to fit residues: 112.2242 Evaluate side-chains 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain D residue 1 MET 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 E residue 72 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 5 optimal weight: 0.0670 chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 overall best weight: 6.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086032 restraints weight = 10191.630| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.49 r_work: 0.3149 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 6950 Z= 0.322 Angle : 0.649 9.531 9320 Z= 0.351 Chirality : 0.053 0.129 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.562 20.967 990 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.20 % Allowed : 22.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.005 TYR D 39 PHE 0.019 0.005 PHE A 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 6950) covalent geometry : angle 0.64879 ( 9320) hydrogen bonds : bond 0.02379 ( 144) hydrogen bonds : angle 5.62974 ( 432) ********************** 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 191 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.293 Fit side-chains REVERT: A 2 ASP cc_start: 0.8242 (m-30) cc_final: 0.7874 (m-30) REVERT: A 5 MET cc_start: 0.8337 (ttm) cc_final: 0.8028 (ttm) REVERT: A 20 GLU cc_start: 0.8567 (tt0) cc_final: 0.8088 (tt0) REVERT: A 65 ASN cc_start: 0.9148 (m110) cc_final: 0.8857 (m110) REVERT: A 98 ASP cc_start: 0.8453 (m-30) cc_final: 0.8246 (m-30) REVERT: C 2 ASP cc_start: 0.8050 (m-30) cc_final: 0.7596 (m-30) REVERT: C 61 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: D 2 ASP cc_start: 0.8595 (m-30) cc_final: 0.8256 (m-30) REVERT: E 61 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: F 61 GLU cc_start: 0.8419 (mp0) cc_final: 0.8045 (mp0) REVERT: G 1 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.5978 (tmm) REVERT: G 35 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: G 61 GLU cc_start: 0.8075 (mp0) cc_final: 0.7347 (mp0) REVERT: H 2 ASP cc_start: 0.8640 (m-30) cc_final: 0.8067 (m-30) REVERT: H 61 GLU cc_start: 0.8210 (mp0) cc_final: 0.7366 (mp0) REVERT: H 79 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8606 (tm-30) REVERT: I 2 ASP cc_start: 0.8492 (m-30) cc_final: 0.8074 (m-30) REVERT: I 65 ASN cc_start: 0.8721 (m110) cc_final: 0.8466 (m-40) REVERT: I 79 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: J 2 ASP cc_start: 0.8452 (m-30) cc_final: 0.8152 (m-30) REVERT: J 61 GLU cc_start: 0.8373 (mp0) cc_final: 0.8051 (mp0) REVERT: J 65 ASN cc_start: 0.8693 (m110) cc_final: 0.8128 (m110) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.5948 time to fit residues: 111.9160 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 : 0.268 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain D residue 1 MET 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 E residue 72 THR 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 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 18 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.085231 restraints weight = 10312.732| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.49 r_work: 0.3133 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 6950 Z= 0.356 Angle : 0.670 9.546 9320 Z= 0.363 Chirality : 0.054 0.130 1160 Planarity : 0.003 0.020 1170 Dihedral : 5.698 21.977 990 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.78 % Allowed : 22.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.58 (0.23), 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 TYR 0.021 0.005 TYR F 39 PHE 0.021 0.005 PHE A 4 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00784 ( 6950) covalent geometry : angle 0.67026 ( 9320) hydrogen bonds : bond 0.02464 ( 144) hydrogen bonds : angle 5.69073 ( 432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.36 seconds wall clock time: 45 minutes 27.37 seconds (2727.37 seconds total)