Starting phenix.real_space_refine on Fri Aug 22 18:26:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.map" model { file = "/net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adw_15372/08_2025/8adw_15372.cif" } resolution = 2.95 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= 0.011 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 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: 10 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "C" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "G" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "H" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "I" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "J" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 6920 At special positions: 0 Unit cell: (143.85, 139.65, 45.15, 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: 0.55 Conformation dependent library (CDL) restraints added in 435.4 milliseconds Enol-peptide restraints added in 715.3 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 21 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.745A pdb=" N PHE A 4 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 4 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE C 4 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE D 4 " --> pdb=" O MET E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.246A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 19 " --> pdb=" O GLU E 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 32 removed outlier: 6.361A pdb=" N ALA A 27 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA B 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 29 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY A 31 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 27 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA C 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 31 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 27 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA D 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 29 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS D 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C 31 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA E 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS E 32 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY D 31 " --> pdb=" O LYS E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.740A pdb=" N GLY B 36 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 36 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 36 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY E 36 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.280A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 74 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 87 through 95 removed outlier: 6.098A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL B 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY C 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL D 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY E 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.752A pdb=" N PHE F 4 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE G 4 " --> pdb=" O MET H 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE H 4 " --> pdb=" O MET I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE I 4 " --> pdb=" O MET J 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 15 through 20 removed outlier: 6.249A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA G 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'F' and resid 27 through 32 removed outlier: 6.361A pdb=" N ALA F 27 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA G 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 29 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS G 32 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY F 31 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA G 27 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA H 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA G 29 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS H 32 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY G 31 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA H 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA I 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA H 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS I 32 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY H 31 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA I 27 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 30 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA I 29 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS J 32 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 6.739A pdb=" N GLY G 36 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY H 36 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY I 36 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY J 36 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 48 through 55 Processing sheet with id=AB8, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB9, first strand: chain 'F' and resid 70 through 71 removed outlier: 6.274A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.237A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL J 77 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 83 removed outlier: 6.609A pdb=" N VAL F 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL H 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL I 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 95 removed outlier: 6.093A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA G 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL G 95 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE F 94 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA H 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA G 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY H 93 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR G 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL H 95 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE G 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY I 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR H 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL I 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE H 94 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N VAL J 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE I 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 152 hydrogen bonds defined for protein. 456 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: 1.10 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1423 1.32 - 1.44: 1262 1.44 - 1.56: 4225 1.56 - 1.68: 0 1.68 - 1.80: 40 Bond restraints: 6950 Sorted by residual: bond pdb=" CA LYS F 80 " pdb=" C LYS F 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.44e+01 bond pdb=" CA LYS G 80 " pdb=" C LYS G 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" CA LYS H 80 " pdb=" C LYS H 80 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.24e-02 6.50e+03 1.41e+01 bond pdb=" CA LYS J 80 " pdb=" C LYS J 80 " ideal model delta sigma weight residual 1.521 1.475 0.046 1.24e-02 6.50e+03 1.38e+01 bond pdb=" CA LYS I 80 " pdb=" C LYS I 80 " ideal model delta sigma weight residual 1.521 1.475 0.046 1.24e-02 6.50e+03 1.36e+01 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 8676 2.52 - 5.05: 525 5.05 - 7.57: 57 7.57 - 10.09: 52 10.09 - 12.62: 10 Bond angle restraints: 9320 Sorted by residual: angle pdb=" N LYS A 60 " pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 112.12 102.90 9.22 1.34e+00 5.57e-01 4.74e+01 angle pdb=" N LYS B 60 " pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N LYS J 60 " pdb=" CA LYS J 60 " pdb=" C LYS J 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N LYS E 60 " pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 112.12 102.91 9.21 1.34e+00 5.57e-01 4.72e+01 angle pdb=" N LYS H 60 " pdb=" CA LYS H 60 " pdb=" C LYS H 60 " ideal model delta sigma weight residual 112.12 102.92 9.20 1.34e+00 5.57e-01 4.71e+01 ... (remaining 9315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3495 17.81 - 35.62: 335 35.62 - 53.42: 250 53.42 - 71.23: 85 71.23 - 89.04: 15 Dihedral angle restraints: 4180 sinusoidal: 1490 harmonic: 2690 Sorted by residual: dihedral pdb=" CB GLU A 57 " pdb=" CG GLU A 57 " pdb=" CD GLU A 57 " pdb=" OE1 GLU A 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 57 " pdb=" CG GLU E 57 " pdb=" CD GLU E 57 " pdb=" OE1 GLU E 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " pdb=" CD GLU B 57 " pdb=" OE1 GLU B 57 " ideal model delta sinusoidal sigma weight residual 0.00 -89.04 89.04 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 866 0.066 - 0.132: 229 0.132 - 0.198: 40 0.198 - 0.263: 10 0.263 - 0.329: 15 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA PHE J 94 " pdb=" N PHE J 94 " pdb=" C PHE J 94 " pdb=" CB PHE J 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA PHE H 94 " pdb=" N PHE H 94 " pdb=" C PHE H 94 " pdb=" CB PHE H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PHE D 94 " pdb=" N PHE D 94 " pdb=" C PHE D 94 " pdb=" CB PHE D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1157 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 60 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS F 60 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS F 60 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU F 61 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 60 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C LYS B 60 " 0.066 2.00e-02 2.50e+03 pdb=" O LYS B 60 " -0.025 2.00e-02 2.50e+03 pdb=" N GLU B 61 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 60 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C LYS I 60 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS I 60 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU I 61 " 0.022 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3280 2.96 - 3.44: 6194 3.44 - 3.93: 11912 3.93 - 4.41: 14300 4.41 - 4.90: 25161 Nonbonded interactions: 60847 Sorted by model distance: nonbonded pdb=" O GLY F 84 " pdb=" O ALA G 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY G 84 " pdb=" O ALA H 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY I 84 " pdb=" O ALA J 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY H 84 " pdb=" O ALA I 85 " model vdw 2.469 3.040 nonbonded pdb=" O GLY B 84 " pdb=" O ALA C 85 " model vdw 2.472 3.040 ... (remaining 60842 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: 0.03 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: 0.920 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.009 0.060 6950 Z= 0.679 Angle : 1.463 12.618 9320 Z= 0.911 Chirality : 0.073 0.329 1160 Planarity : 0.006 0.038 1170 Dihedral : 22.424 89.039 2480 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 23.33 % Allowed : 11.45 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -4.02 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 39 PHE 0.052 0.009 PHE F 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 6950) covalent geometry : angle 1.46296 ( 9320) hydrogen bonds : bond 0.15572 ( 152) hydrogen bonds : angle 8.63332 ( 456) *********************** 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 310 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 149 time to evaluate : 0.168 Fit side-chains REVERT: A 28 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 83 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6969 (mm-30) REVERT: A 98 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: B 92 THR cc_start: 0.8341 (m) cc_final: 0.7940 (p) REVERT: C 5 MET cc_start: 0.7423 (ttm) cc_final: 0.7190 (ttt) REVERT: D 28 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: D 92 THR cc_start: 0.8456 (m) cc_final: 0.8055 (p) REVERT: D 98 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6970 (m-30) REVERT: E 5 MET cc_start: 0.7329 (ttm) cc_final: 0.7068 (ttt) REVERT: E 10 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.6784 (pttp) REVERT: E 12 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.5538 (pmtt) REVERT: F 5 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7588 (ttt) REVERT: F 98 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: H 5 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7216 (ttt) REVERT: H 20 GLU cc_start: 0.7452 (mp0) cc_final: 0.7242 (mp0) REVERT: I 28 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: I 98 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: J 5 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7068 (ttt) REVERT: J 10 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.6863 (pttm) REVERT: J 12 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.5668 (pmtt) REVERT: J 20 GLU cc_start: 0.7307 (mp0) cc_final: 0.7093 (mp0) outliers start: 161 outliers final: 17 residues processed: 245 average time/residue: 0.5293 time to fit residues: 136.0237 Evaluate side-chains 140 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 5 MET Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 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 = 0.4249 r_free = 0.4249 target = 0.148035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.127493 restraints weight = 8953.926| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.31 r_work: 0.3888 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6950 Z= 0.155 Angle : 0.600 4.789 9320 Z= 0.333 Chirality : 0.052 0.126 1160 Planarity : 0.002 0.008 1170 Dihedral : 9.669 57.101 1062 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.68 % Allowed : 23.62 % Favored : 68.70 % 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: -3.69 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.014 0.003 PHE H 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 6950) covalent geometry : angle 0.60028 ( 9320) hydrogen bonds : bond 0.02965 ( 152) hydrogen bonds : angle 5.18222 ( 456) *********************** 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 158 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.206 Fit side-chains REVERT: A 13 GLU cc_start: 0.7440 (mp0) cc_final: 0.6500 (mm-30) REVERT: A 28 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 98 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: C 5 MET cc_start: 0.8149 (ttm) cc_final: 0.7874 (ttt) REVERT: D 28 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: E 2 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: F 13 GLU cc_start: 0.7405 (mp0) cc_final: 0.6492 (mm-30) REVERT: F 98 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: G 12 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6008 (ttmm) REVERT: G 98 ASP cc_start: 0.7304 (m-30) cc_final: 0.6985 (m-30) REVERT: H 20 GLU cc_start: 0.8077 (mp0) cc_final: 0.7860 (mp0) REVERT: I 28 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: J 2 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: J 20 GLU cc_start: 0.7876 (mp0) cc_final: 0.7628 (mp0) outliers start: 53 outliers final: 18 residues processed: 140 average time/residue: 0.4657 time to fit residues: 69.2491 Evaluate side-chains 123 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 68 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.141929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.121498 restraints weight = 9017.316| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.25 r_work: 0.3811 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2789 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= 0.249 Angle : 0.622 4.380 9320 Z= 0.347 Chirality : 0.052 0.137 1160 Planarity : 0.002 0.008 1170 Dihedral : 9.024 59.487 1029 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 7.25 % Allowed : 25.07 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR B 39 PHE 0.014 0.004 PHE C 4 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6950) covalent geometry : angle 0.62173 ( 9320) hydrogen bonds : bond 0.03079 ( 152) hydrogen bonds : angle 5.23861 ( 456) *********************** 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 166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 12 LYS cc_start: 0.6614 (OUTLIER) cc_final: 0.5646 (ttmm) REVERT: B 13 GLU cc_start: 0.8107 (mp0) cc_final: 0.7697 (mp0) REVERT: B 58 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8042 (tmtm) REVERT: C 5 MET cc_start: 0.8265 (ttm) cc_final: 0.7975 (ttt) REVERT: C 98 ASP cc_start: 0.7382 (m-30) cc_final: 0.7079 (m-30) REVERT: E 5 MET cc_start: 0.8484 (ttp) cc_final: 0.8210 (ttt) REVERT: F 12 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6056 (tppt) REVERT: F 13 GLU cc_start: 0.7534 (mp0) cc_final: 0.7117 (mm-30) REVERT: G 12 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6193 (ttmm) REVERT: H 98 ASP cc_start: 0.7355 (m-30) cc_final: 0.7107 (m-30) REVERT: I 5 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8229 (ttp) REVERT: I 28 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7753 (mt-10) outliers start: 50 outliers final: 22 residues processed: 150 average time/residue: 0.5244 time to fit residues: 82.8441 Evaluate side-chains 138 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4128 r_free = 0.4128 target = 0.138753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.118916 restraints weight = 9310.444| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.22 r_work: 0.3763 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 6950 Z= 0.353 Angle : 0.715 6.887 9320 Z= 0.400 Chirality : 0.054 0.139 1160 Planarity : 0.003 0.017 1170 Dihedral : 8.994 56.372 1022 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 7.68 % Allowed : 26.67 % Favored : 65.65 % 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 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.003 TYR C 39 PHE 0.018 0.004 PHE D 4 HIS 0.003 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00760 ( 6950) covalent geometry : angle 0.71503 ( 9320) hydrogen bonds : bond 0.03303 ( 152) hydrogen bonds : angle 5.26944 ( 456) *********************** 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 179 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.233 Fit side-chains REVERT: B 12 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.5960 (ttmm) REVERT: B 13 GLU cc_start: 0.7951 (mp0) cc_final: 0.7533 (mp0) REVERT: B 58 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8217 (tmtm) REVERT: C 5 MET cc_start: 0.8284 (ttm) cc_final: 0.7938 (ttt) REVERT: C 98 ASP cc_start: 0.7482 (m-30) cc_final: 0.7080 (m-30) REVERT: D 98 ASP cc_start: 0.7592 (p0) cc_final: 0.7301 (p0) REVERT: E 2 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6997 (p0) REVERT: F 13 GLU cc_start: 0.7583 (mp0) cc_final: 0.6799 (tp30) REVERT: G 12 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.6050 (ttmm) REVERT: H 98 ASP cc_start: 0.7449 (m-30) cc_final: 0.7021 (m-30) REVERT: I 83 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6279 (mt-10) REVERT: I 98 ASP cc_start: 0.7571 (p0) cc_final: 0.7280 (p0) REVERT: J 2 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6973 (p0) outliers start: 53 outliers final: 25 residues processed: 159 average time/residue: 0.4688 time to fit residues: 78.9088 Evaluate side-chains 152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4209 r_free = 0.4209 target = 0.143529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.123945 restraints weight = 9193.750| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.18 r_work: 0.3866 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6950 Z= 0.160 Angle : 0.595 7.277 9320 Z= 0.321 Chirality : 0.051 0.136 1160 Planarity : 0.002 0.014 1170 Dihedral : 7.672 55.469 1016 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 6.67 % Allowed : 28.12 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.40 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.012 0.003 PHE H 94 HIS 0.001 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6950) covalent geometry : angle 0.59463 ( 9320) hydrogen bonds : bond 0.02432 ( 152) hydrogen bonds : angle 4.75589 ( 456) *********************** 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 175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6378 (tp30) REVERT: B 12 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6013 (ttmm) REVERT: B 58 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8053 (tmtm) REVERT: B 61 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7646 (tm-30) REVERT: C 2 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: C 5 MET cc_start: 0.8238 (ttm) cc_final: 0.7987 (ttt) REVERT: C 98 ASP cc_start: 0.7488 (m-30) cc_final: 0.6969 (m-30) REVERT: D 98 ASP cc_start: 0.7481 (p0) cc_final: 0.7096 (p0) REVERT: E 2 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6968 (p0) REVERT: E 5 MET cc_start: 0.8492 (ttp) cc_final: 0.8202 (ttt) REVERT: F 12 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6159 (tppt) REVERT: F 13 GLU cc_start: 0.7439 (mp0) cc_final: 0.7127 (tp30) REVERT: G 12 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6073 (ttmm) REVERT: G 83 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: H 2 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: H 98 ASP cc_start: 0.7476 (m-30) cc_final: 0.6945 (m-30) REVERT: I 83 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6286 (mt-10) REVERT: I 98 ASP cc_start: 0.7467 (p0) cc_final: 0.7068 (p0) REVERT: J 2 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.7037 (p0) outliers start: 46 outliers final: 24 residues processed: 163 average time/residue: 0.4535 time to fit residues: 78.1509 Evaluate side-chains 159 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 12 LYS Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 79 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 = 0.4146 r_free = 0.4146 target = 0.139288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119568 restraints weight = 9318.419| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.20 r_work: 0.3781 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6950 Z= 0.333 Angle : 0.705 6.068 9320 Z= 0.388 Chirality : 0.054 0.147 1160 Planarity : 0.003 0.013 1170 Dihedral : 8.128 57.510 1016 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 7.25 % Allowed : 28.70 % Favored : 64.06 % 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: -3.54 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.016 0.004 PHE D 4 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00716 ( 6950) covalent geometry : angle 0.70473 ( 9320) hydrogen bonds : bond 0.03135 ( 152) hydrogen bonds : angle 5.14215 ( 456) *********************** 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 172 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.263 Fit side-chains REVERT: A 13 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6327 (tp30) REVERT: B 12 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.5955 (ttmm) REVERT: B 58 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8094 (tmtm) REVERT: C 98 ASP cc_start: 0.7719 (m-30) cc_final: 0.7212 (m-30) REVERT: D 98 ASP cc_start: 0.7570 (p0) cc_final: 0.7224 (p0) REVERT: E 2 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7020 (p0) REVERT: E 5 MET cc_start: 0.8425 (ttp) cc_final: 0.8153 (ttt) REVERT: F 13 GLU cc_start: 0.7540 (mp0) cc_final: 0.6867 (tp30) REVERT: G 12 LYS cc_start: 0.6381 (OUTLIER) cc_final: 0.5951 (ttmm) REVERT: H 2 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: H 98 ASP cc_start: 0.7737 (m-30) cc_final: 0.7226 (m-30) REVERT: I 2 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: I 98 ASP cc_start: 0.7550 (p0) cc_final: 0.7208 (p0) REVERT: J 2 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6963 (p0) outliers start: 50 outliers final: 22 residues processed: 152 average time/residue: 0.4632 time to fit residues: 74.6963 Evaluate side-chains 152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 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: 3.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4232 r_free = 0.4232 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.125303 restraints weight = 9154.933| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.20 r_work: 0.3875 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6950 Z= 0.165 Angle : 0.615 6.448 9320 Z= 0.331 Chirality : 0.051 0.137 1160 Planarity : 0.002 0.015 1170 Dihedral : 7.492 58.605 1016 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 6.23 % Allowed : 30.72 % Favored : 63.04 % 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: -3.41 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR I 39 PHE 0.012 0.003 PHE C 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6950) covalent geometry : angle 0.61545 ( 9320) hydrogen bonds : bond 0.02379 ( 152) hydrogen bonds : angle 4.69847 ( 456) *********************** 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 179 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.227 Fit side-chains REVERT: A 13 GLU cc_start: 0.7056 (mp0) cc_final: 0.6422 (mm-30) REVERT: B 12 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6035 (ttmm) REVERT: B 58 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8057 (tmtm) REVERT: C 2 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6949 (m-30) REVERT: C 5 MET cc_start: 0.8215 (ttm) cc_final: 0.7883 (ttt) REVERT: C 98 ASP cc_start: 0.7645 (m-30) cc_final: 0.7023 (m-30) REVERT: D 2 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: D 98 ASP cc_start: 0.7431 (p0) cc_final: 0.7021 (p0) REVERT: E 5 MET cc_start: 0.8426 (ttp) cc_final: 0.7406 (tpt) REVERT: F 13 GLU cc_start: 0.7449 (mp0) cc_final: 0.6869 (tp30) REVERT: G 83 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: H 2 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: H 61 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7380 (tp30) REVERT: H 98 ASP cc_start: 0.7672 (m-30) cc_final: 0.7053 (m-30) REVERT: I 2 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7394 (m-30) REVERT: I 83 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6316 (mm-30) REVERT: I 98 ASP cc_start: 0.7417 (p0) cc_final: 0.7013 (p0) outliers start: 43 outliers final: 18 residues processed: 163 average time/residue: 0.5161 time to fit residues: 88.7068 Evaluate side-chains 157 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.139365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119713 restraints weight = 9395.965| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.17 r_work: 0.3795 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 6950 Z= 0.303 Angle : 0.727 7.898 9320 Z= 0.397 Chirality : 0.053 0.165 1160 Planarity : 0.003 0.018 1170 Dihedral : 7.786 59.817 1012 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.09 % Allowed : 31.16 % Favored : 62.75 % 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: -3.48 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 39 PHE 0.015 0.004 PHE D 4 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 6950) covalent geometry : angle 0.72729 ( 9320) hydrogen bonds : bond 0.03002 ( 152) hydrogen bonds : angle 5.15820 ( 456) *********************** 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 173 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.273 Fit side-chains REVERT: A 13 GLU cc_start: 0.7128 (mp0) cc_final: 0.6355 (tp30) REVERT: B 12 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6048 (ttmm) REVERT: B 58 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8147 (tmtm) REVERT: C 2 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7067 (m-30) REVERT: C 98 ASP cc_start: 0.7817 (m-30) cc_final: 0.7175 (m-30) REVERT: D 2 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: D 98 ASP cc_start: 0.7484 (p0) cc_final: 0.7126 (p0) REVERT: E 5 MET cc_start: 0.8500 (ttp) cc_final: 0.8226 (ttt) REVERT: F 13 GLU cc_start: 0.7386 (mp0) cc_final: 0.6679 (tp30) REVERT: G 61 GLU cc_start: 0.7540 (tp30) cc_final: 0.7302 (tp30) REVERT: H 2 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: H 98 ASP cc_start: 0.7751 (m-30) cc_final: 0.7180 (m-30) REVERT: I 2 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: I 83 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6405 (mm-30) REVERT: I 98 ASP cc_start: 0.7468 (p0) cc_final: 0.7125 (p0) outliers start: 42 outliers final: 18 residues processed: 161 average time/residue: 0.5156 time to fit residues: 87.6707 Evaluate side-chains 155 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 70 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4198 r_free = 0.4198 target = 0.141846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122627 restraints weight = 9435.825| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.18 r_work: 0.3844 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6950 Z= 0.201 Angle : 0.682 6.946 9320 Z= 0.367 Chirality : 0.052 0.142 1160 Planarity : 0.002 0.012 1170 Dihedral : 7.403 58.227 1012 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.78 % Allowed : 33.04 % Favored : 62.17 % 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: -3.42 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 39 PHE 0.017 0.003 PHE J 4 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6950) covalent geometry : angle 0.68198 ( 9320) hydrogen bonds : bond 0.02557 ( 152) hydrogen bonds : angle 4.90950 ( 456) *********************** 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 162 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.341 Fit side-chains REVERT: A 13 GLU cc_start: 0.7097 (mp0) cc_final: 0.6492 (mm-30) REVERT: B 12 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6065 (ttmm) REVERT: B 58 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8045 (tmtm) REVERT: C 2 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: C 98 ASP cc_start: 0.7813 (m-30) cc_final: 0.7146 (m-30) REVERT: D 98 ASP cc_start: 0.7520 (p0) cc_final: 0.7103 (p0) REVERT: E 1 MET cc_start: 0.4549 (tmm) cc_final: 0.4259 (tmm) REVERT: E 5 MET cc_start: 0.8431 (ttp) cc_final: 0.8157 (ttt) REVERT: F 13 GLU cc_start: 0.7345 (mp0) cc_final: 0.6754 (tp30) REVERT: H 2 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: H 98 ASP cc_start: 0.7727 (m-30) cc_final: 0.7171 (m-30) REVERT: I 2 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: I 83 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6364 (mm-30) REVERT: I 98 ASP cc_start: 0.7514 (p0) cc_final: 0.7165 (p0) REVERT: J 1 MET cc_start: 0.4614 (tmm) cc_final: 0.4298 (tmm) outliers start: 33 outliers final: 20 residues processed: 152 average time/residue: 0.5207 time to fit residues: 84.0019 Evaluate side-chains 152 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4125 r_free = 0.4125 target = 0.138149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118945 restraints weight = 9815.186| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.14 r_work: 0.3758 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 6950 Z= 0.375 Angle : 0.801 8.149 9320 Z= 0.436 Chirality : 0.055 0.193 1160 Planarity : 0.003 0.018 1170 Dihedral : 7.754 59.252 1010 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.49 % Allowed : 33.19 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR A 39 PHE 0.031 0.005 PHE J 4 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00814 ( 6950) covalent geometry : angle 0.80074 ( 9320) hydrogen bonds : bond 0.03158 ( 152) hydrogen bonds : angle 5.32392 ( 456) ********************** 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 166 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.282 Fit side-chains REVERT: A 13 GLU cc_start: 0.7073 (mp0) cc_final: 0.6372 (tp30) REVERT: A 61 GLU cc_start: 0.7437 (tp30) cc_final: 0.6625 (tp30) REVERT: B 12 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6114 (ttmm) REVERT: B 58 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8243 (tmtm) REVERT: B 61 GLU cc_start: 0.7567 (tp30) cc_final: 0.7297 (tp30) REVERT: C 98 ASP cc_start: 0.7938 (m-30) cc_final: 0.7302 (m-30) REVERT: D 98 ASP cc_start: 0.7629 (p0) cc_final: 0.7206 (p0) REVERT: E 5 MET cc_start: 0.8500 (ttp) cc_final: 0.8231 (ttt) REVERT: F 13 GLU cc_start: 0.7367 (mp0) cc_final: 0.6680 (tp30) REVERT: F 61 GLU cc_start: 0.7474 (tp30) cc_final: 0.6471 (tp30) REVERT: G 61 GLU cc_start: 0.7400 (tp30) cc_final: 0.7184 (tp30) REVERT: H 2 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7175 (m-30) REVERT: H 98 ASP cc_start: 0.7866 (m-30) cc_final: 0.7292 (m-30) REVERT: I 2 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: I 83 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6457 (mm-30) REVERT: I 98 ASP cc_start: 0.7612 (p0) cc_final: 0.7186 (p0) outliers start: 31 outliers final: 20 residues processed: 155 average time/residue: 0.5560 time to fit residues: 90.9246 Evaluate side-chains 157 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 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 = 0.4147 r_free = 0.4147 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120523 restraints weight = 9786.338| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.16 r_work: 0.3784 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6950 Z= 0.291 Angle : 0.755 7.645 9320 Z= 0.407 Chirality : 0.053 0.159 1160 Planarity : 0.003 0.017 1170 Dihedral : 7.467 57.731 1008 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.91 % Allowed : 34.35 % Favored : 61.74 % 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 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR A 39 PHE 0.024 0.004 PHE J 4 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 6950) covalent geometry : angle 0.75463 ( 9320) hydrogen bonds : bond 0.02876 ( 152) hydrogen bonds : angle 5.21469 ( 456) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.85 seconds wall clock time: 42 minutes 58.49 seconds (2578.49 seconds total)