Starting phenix.real_space_refine on Fri Dec 27 22:15:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.map" model { file = "/net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adv_15371/12_2024/8adv_15371.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 4320 2.51 5 N 1200 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.69, per 1000 atoms: 0.39 Number of scatterers: 6920 At special positions: 0 Unit cell: (120.75, 129.15, 51.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1380 8.00 N 1200 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.280A pdb=" N VAL A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA C 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU E 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL E 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA G 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA E 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU G 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL G 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA I 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS C 34 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 35 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 34 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 35 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS G 34 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 35 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS I 34 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 35 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 58 removed outlier: 9.280A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AB2, first strand: chain 'A' and resid 82 through 83 removed outlier: 5.969A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL C 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL E 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL G 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY C 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS E 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS G 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY G 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS I 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL G 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.279A pdb=" N VAL B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA D 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU D 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA F 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA D 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU F 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA H 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA F 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU H 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL H 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA J 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA H 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU J 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA H 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS D 34 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 35 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 34 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 35 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS H 34 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU F 35 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS J 34 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 35 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 58 removed outlier: 9.279A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL F 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL H 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY F 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR H 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS J 58 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU H 57 " --> pdb=" O LYS J 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 79 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.968A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL D 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL F 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL H 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS J 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 144 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.19 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.740 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.190 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.650 ------------------------------------------------------------------------------- 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= 0.378 Angle : 0.636 4.991 9320 Z= 0.365 Chirality : 0.053 0.165 1160 Planarity : 0.002 0.009 1170 Dihedral : 12.650 76.203 2480 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.45 % Allowed : 0.00 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 PHE 0.020 0.005 PHE G 4 TYR 0.015 0.004 TYR H 39 *********************** 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 : 0.769 Fit side-chains REVERT: A 5 MET cc_start: 0.7766 (ttm) cc_final: 0.7468 (ttm) REVERT: B 65 ASN cc_start: 0.8795 (m110) cc_final: 0.8525 (m110) REVERT: C 61 GLU cc_start: 0.7573 (mp0) cc_final: 0.7114 (mp0) REVERT: E 5 MET cc_start: 0.7884 (ttm) cc_final: 0.7680 (ttm) REVERT: E 65 ASN cc_start: 0.8599 (m110) cc_final: 0.8387 (m-40) REVERT: G 61 GLU cc_start: 0.7429 (mp0) cc_final: 0.7210 (mp0) REVERT: I 2 ASP cc_start: 0.8041 (m-30) cc_final: 0.7718 (m-30) REVERT: I 65 ASN cc_start: 0.8531 (m110) cc_final: 0.8251 (m-40) REVERT: J 65 ASN cc_start: 0.8568 (m110) cc_final: 0.8077 (m110) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 1.2971 time to fit residues: 213.7156 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 : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6950 Z= 0.328 Angle : 0.580 5.859 9320 Z= 0.320 Chirality : 0.051 0.128 1160 Planarity : 0.002 0.015 1170 Dihedral : 5.309 17.394 990 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.90 % Allowed : 12.46 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE C 4 TYR 0.018 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.821 Fit side-chains REVERT: A 5 MET cc_start: 0.7556 (ttm) cc_final: 0.7246 (ttm) REVERT: A 46 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 65 ASN cc_start: 0.8756 (m110) cc_final: 0.8501 (m110) REVERT: C 46 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 61 GLU cc_start: 0.7744 (mp0) cc_final: 0.7131 (mp0) REVERT: E 61 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: G 61 GLU cc_start: 0.7568 (mp0) cc_final: 0.7252 (mp0) REVERT: H 61 GLU cc_start: 0.7874 (mp0) cc_final: 0.7562 (mp0) REVERT: I 65 ASN cc_start: 0.8570 (m110) cc_final: 0.8288 (m-40) REVERT: J 65 ASN cc_start: 0.8572 (m110) cc_final: 0.8102 (m110) outliers start: 20 outliers final: 7 residues processed: 171 average time/residue: 1.2306 time to fit residues: 221.1451 Evaluate side-chains 173 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6950 Z= 0.372 Angle : 0.585 6.232 9320 Z= 0.323 Chirality : 0.052 0.127 1160 Planarity : 0.002 0.013 1170 Dihedral : 5.319 18.265 990 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.51 % Allowed : 14.20 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.017 0.004 PHE C 4 TYR 0.019 0.004 TYR B 39 *********************** 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: 38 poor density : 166 time to evaluate : 0.799 Fit side-chains REVERT: A 5 MET cc_start: 0.7593 (ttm) cc_final: 0.7271 (ttm) REVERT: B 2 ASP cc_start: 0.8060 (m-30) cc_final: 0.7740 (m-30) REVERT: D 1 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6374 (ttt) REVERT: D 2 ASP cc_start: 0.8116 (m-30) cc_final: 0.7796 (m-30) REVERT: G 61 GLU cc_start: 0.7608 (mp0) cc_final: 0.7327 (mp0) REVERT: H 2 ASP cc_start: 0.8022 (m-30) cc_final: 0.7563 (m-30) REVERT: H 61 GLU cc_start: 0.7837 (mp0) cc_final: 0.7253 (mp0) REVERT: I 61 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: I 65 ASN cc_start: 0.8535 (m110) cc_final: 0.8250 (m-40) REVERT: J 2 ASP cc_start: 0.8004 (m-30) cc_final: 0.7783 (m-30) REVERT: J 65 ASN cc_start: 0.8575 (m110) cc_final: 0.8141 (m110) outliers start: 38 outliers final: 20 residues processed: 179 average time/residue: 1.1878 time to fit residues: 223.6758 Evaluate side-chains 185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1607 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= 0.473 Angle : 0.626 6.669 9320 Z= 0.344 Chirality : 0.053 0.129 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.545 20.547 990 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.78 % Allowed : 17.54 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.018 0.005 PHE A 4 TYR 0.021 0.005 TYR I 39 *********************** 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 195 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.834 Fit side-chains REVERT: A 5 MET cc_start: 0.7611 (ttm) cc_final: 0.7293 (ttm) REVERT: A 65 ASN cc_start: 0.8913 (m110) cc_final: 0.8641 (m110) REVERT: B 2 ASP cc_start: 0.8057 (m-30) cc_final: 0.7757 (m-30) REVERT: C 2 ASP cc_start: 0.7832 (m-30) cc_final: 0.7580 (m-30) REVERT: C 61 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: D 2 ASP cc_start: 0.8145 (m-30) cc_final: 0.7854 (m-30) REVERT: G 1 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6208 (tmm) REVERT: G 61 GLU cc_start: 0.7699 (mp0) cc_final: 0.7188 (mp0) REVERT: H 2 ASP cc_start: 0.8070 (m-30) cc_final: 0.7617 (m-30) REVERT: H 61 GLU cc_start: 0.7841 (mp0) cc_final: 0.7169 (mp0) REVERT: I 2 ASP cc_start: 0.8102 (m-30) cc_final: 0.7746 (m-30) REVERT: I 61 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: I 65 ASN cc_start: 0.8482 (m110) cc_final: 0.8205 (m-40) REVERT: J 2 ASP cc_start: 0.8065 (m-30) cc_final: 0.7830 (m-30) REVERT: J 61 GLU cc_start: 0.8055 (mp0) cc_final: 0.7819 (mp0) REVERT: J 65 ASN cc_start: 0.8605 (m110) cc_final: 0.8135 (m110) outliers start: 33 outliers final: 21 residues processed: 175 average time/residue: 1.2256 time to fit residues: 225.6639 Evaluate side-chains 184 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6950 Z= 0.159 Angle : 0.493 6.781 9320 Z= 0.270 Chirality : 0.049 0.120 1160 Planarity : 0.001 0.006 1170 Dihedral : 4.915 15.307 990 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.62 % Allowed : 19.86 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.014 0.002 PHE D 4 TYR 0.007 0.002 TYR I 39 *********************** 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 188 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.791 Fit side-chains REVERT: A 5 MET cc_start: 0.7361 (ttm) cc_final: 0.7076 (ttm) REVERT: A 65 ASN cc_start: 0.8865 (m110) cc_final: 0.8616 (m110) REVERT: B 5 MET cc_start: 0.7317 (ttm) cc_final: 0.7045 (ttm) REVERT: C 2 ASP cc_start: 0.7667 (m-30) cc_final: 0.7400 (m-30) REVERT: C 61 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: D 1 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6017 (ttt) REVERT: D 2 ASP cc_start: 0.8100 (m-30) cc_final: 0.7791 (m-30) REVERT: D 99 GLN cc_start: 0.6083 (mt0) cc_final: 0.5540 (mt0) REVERT: F 20 GLU cc_start: 0.7902 (tt0) cc_final: 0.7652 (tm-30) REVERT: G 1 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.6136 (tmm) REVERT: G 35 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: G 61 GLU cc_start: 0.7371 (mp0) cc_final: 0.7097 (mp0) REVERT: H 61 GLU cc_start: 0.7779 (mp0) cc_final: 0.7212 (mp0) REVERT: I 65 ASN cc_start: 0.8524 (m110) cc_final: 0.8261 (m-40) REVERT: J 65 ASN cc_start: 0.8616 (m110) cc_final: 0.8179 (m110) outliers start: 25 outliers final: 10 residues processed: 174 average time/residue: 1.2105 time to fit residues: 221.2884 Evaluate side-chains 175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 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 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 0.0870 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 overall best weight: 2.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6950 Z= 0.228 Angle : 0.525 7.986 9320 Z= 0.286 Chirality : 0.050 0.122 1160 Planarity : 0.002 0.010 1170 Dihedral : 4.899 16.573 990 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.77 % Allowed : 21.88 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.013 0.003 PHE C 4 TYR 0.011 0.003 TYR I 39 *********************** 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 185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.822 Fit side-chains REVERT: A 5 MET cc_start: 0.7433 (ttm) cc_final: 0.7172 (ttm) REVERT: A 65 ASN cc_start: 0.8879 (m110) cc_final: 0.8622 (m110) REVERT: B 5 MET cc_start: 0.7487 (ttm) cc_final: 0.7189 (ttm) REVERT: C 2 ASP cc_start: 0.7690 (m-30) cc_final: 0.7390 (m-30) REVERT: C 61 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: D 2 ASP cc_start: 0.8180 (m-30) cc_final: 0.7806 (m-30) REVERT: G 1 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.6139 (tmm) REVERT: G 35 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: H 61 GLU cc_start: 0.7712 (mp0) cc_final: 0.7162 (mp0) REVERT: I 65 ASN cc_start: 0.8518 (m110) cc_final: 0.8265 (m-40) REVERT: J 65 ASN cc_start: 0.8595 (m110) cc_final: 0.8086 (m110) outliers start: 26 outliers final: 15 residues processed: 171 average time/residue: 1.1901 time to fit residues: 214.7683 Evaluate side-chains 177 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B 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 9 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6950 Z= 0.294 Angle : 0.560 8.574 9320 Z= 0.305 Chirality : 0.050 0.124 1160 Planarity : 0.002 0.018 1170 Dihedral : 5.050 17.713 990 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.91 % Allowed : 21.74 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.015 0.004 PHE C 4 TYR 0.014 0.003 TYR I 39 *********************** 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 190 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.862 Fit side-chains REVERT: A 5 MET cc_start: 0.7551 (ttm) cc_final: 0.7254 (ttm) REVERT: A 65 ASN cc_start: 0.8875 (m110) cc_final: 0.8619 (m110) REVERT: B 5 MET cc_start: 0.7547 (ttm) cc_final: 0.7252 (ttm) REVERT: C 2 ASP cc_start: 0.7688 (m-30) cc_final: 0.7369 (m-30) REVERT: C 61 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: D 2 ASP cc_start: 0.8126 (m-30) cc_final: 0.7760 (m-30) REVERT: E 2 ASP cc_start: 0.8228 (m-30) cc_final: 0.7997 (m-30) REVERT: E 61 GLU cc_start: 0.7830 (mp0) cc_final: 0.7611 (mp0) REVERT: G 1 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.6072 (tmm) REVERT: G 20 GLU cc_start: 0.7872 (tt0) cc_final: 0.7506 (tt0) REVERT: G 35 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6974 (tp30) REVERT: H 61 GLU cc_start: 0.7742 (mp0) cc_final: 0.7225 (mp0) REVERT: H 79 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: I 65 ASN cc_start: 0.8515 (m110) cc_final: 0.8281 (m-40) REVERT: J 2 ASP cc_start: 0.8006 (m-30) cc_final: 0.7721 (m-30) REVERT: J 65 ASN cc_start: 0.8573 (m110) cc_final: 0.8057 (m110) outliers start: 27 outliers final: 18 residues processed: 180 average time/residue: 1.2146 time to fit residues: 229.6375 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 : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 9 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1859 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= 0.473 Angle : 0.644 8.847 9320 Z= 0.351 Chirality : 0.053 0.128 1160 Planarity : 0.002 0.013 1170 Dihedral : 5.414 20.704 990 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.64 % Allowed : 22.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.019 0.005 PHE A 4 TYR 0.020 0.005 TYR I 39 *********************** 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 193 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.854 Fit side-chains REVERT: A 5 MET cc_start: 0.7611 (ttm) cc_final: 0.7303 (ttm) REVERT: A 65 ASN cc_start: 0.8884 (m110) cc_final: 0.8624 (m110) REVERT: B 5 MET cc_start: 0.7849 (ttm) cc_final: 0.7568 (ttm) REVERT: C 2 ASP cc_start: 0.7700 (m-30) cc_final: 0.7388 (m-30) REVERT: C 61 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: D 2 ASP cc_start: 0.8162 (m-30) cc_final: 0.7822 (m-30) REVERT: F 1 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.6580 (tmm) REVERT: F 5 MET cc_start: 0.8035 (ttm) cc_final: 0.7658 (ttm) REVERT: G 1 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.6122 (tmm) REVERT: G 20 GLU cc_start: 0.7849 (tt0) cc_final: 0.7469 (tm-30) REVERT: G 35 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: H 2 ASP cc_start: 0.8154 (m-30) cc_final: 0.7704 (m-30) REVERT: H 61 GLU cc_start: 0.7782 (mp0) cc_final: 0.7189 (mp0) REVERT: H 79 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: I 2 ASP cc_start: 0.8113 (m-30) cc_final: 0.7746 (m-30) REVERT: I 65 ASN cc_start: 0.8558 (m110) cc_final: 0.8323 (m-40) REVERT: J 2 ASP cc_start: 0.8086 (m-30) cc_final: 0.7848 (m-30) REVERT: J 61 GLU cc_start: 0.8033 (mp0) cc_final: 0.7753 (mp0) REVERT: J 65 ASN cc_start: 0.8561 (m110) cc_final: 0.8025 (m110) outliers start: 32 outliers final: 21 residues processed: 180 average time/residue: 1.1565 time to fit residues: 219.2079 Evaluate side-chains 186 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 57 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6950 Z= 0.211 Angle : 0.535 8.471 9320 Z= 0.290 Chirality : 0.050 0.124 1160 Planarity : 0.002 0.022 1170 Dihedral : 5.031 16.400 990 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.33 % Allowed : 24.35 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.016 0.003 PHE D 4 TYR 0.009 0.002 TYR D 39 *********************** 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 183 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.768 Fit side-chains REVERT: A 5 MET cc_start: 0.7464 (ttm) cc_final: 0.7185 (ttm) REVERT: A 65 ASN cc_start: 0.8864 (m110) cc_final: 0.8605 (m110) REVERT: B 5 MET cc_start: 0.7477 (ttm) cc_final: 0.7186 (ttm) REVERT: C 61 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: D 2 ASP cc_start: 0.8101 (m-30) cc_final: 0.7758 (m-30) REVERT: E 37 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8426 (t) REVERT: G 1 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.6209 (tmm) REVERT: G 20 GLU cc_start: 0.7819 (tt0) cc_final: 0.7594 (tt0) REVERT: G 35 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: H 2 ASP cc_start: 0.8066 (m-30) cc_final: 0.7592 (m-30) REVERT: H 61 GLU cc_start: 0.7786 (mp0) cc_final: 0.7259 (mp0) REVERT: H 79 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: I 65 ASN cc_start: 0.8620 (m110) cc_final: 0.8392 (m-40) REVERT: J 2 ASP cc_start: 0.7956 (m-30) cc_final: 0.7709 (m-30) REVERT: J 65 ASN cc_start: 0.8556 (m110) cc_final: 0.8023 (m110) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 1.1714 time to fit residues: 214.5071 Evaluate side-chains 180 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B 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 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6950 Z= 0.229 Angle : 0.566 9.072 9320 Z= 0.305 Chirality : 0.050 0.123 1160 Planarity : 0.002 0.015 1170 Dihedral : 4.996 16.502 990 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.75 % Allowed : 24.35 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 PHE 0.014 0.003 PHE C 4 TYR 0.012 0.003 TYR D 39 ********************** 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 180 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.725 Fit side-chains REVERT: A 5 MET cc_start: 0.7484 (ttm) cc_final: 0.7192 (ttm) REVERT: A 65 ASN cc_start: 0.8837 (m110) cc_final: 0.8582 (m110) REVERT: B 5 MET cc_start: 0.7483 (ttm) cc_final: 0.7183 (ttm) REVERT: C 61 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: D 2 ASP cc_start: 0.8111 (m-30) cc_final: 0.7725 (m-30) REVERT: E 37 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (t) REVERT: G 1 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.6129 (tmm) REVERT: G 20 GLU cc_start: 0.7800 (tt0) cc_final: 0.7565 (tt0) REVERT: G 35 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: H 61 GLU cc_start: 0.7786 (mp0) cc_final: 0.7210 (mp0) REVERT: H 79 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: I 65 ASN cc_start: 0.8620 (m110) cc_final: 0.8380 (m-40) REVERT: J 2 ASP cc_start: 0.7971 (m-30) cc_final: 0.7684 (m-30) REVERT: J 65 ASN cc_start: 0.8549 (m110) cc_final: 0.8019 (m110) outliers start: 19 outliers final: 14 residues processed: 173 average time/residue: 1.1659 time to fit residues: 212.5386 Evaluate side-chains 180 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.101944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087000 restraints weight = 10108.075| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.48 r_work: 0.3174 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6950 Z= 0.427 Angle : 0.641 9.264 9320 Z= 0.348 Chirality : 0.052 0.128 1160 Planarity : 0.002 0.017 1170 Dihedral : 5.377 20.028 990 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.04 % Allowed : 24.06 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.23), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.017 0.004 PHE B 4 TYR 0.019 0.005 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.02 seconds wall clock time: 62 minutes 45.03 seconds (3765.03 seconds total)