Starting phenix.real_space_refine on Tue Mar 11 23:05:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adw_15372/03_2025/8adw_15372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adw_15372/03_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_15372/03_2025/8adw_15372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adw_15372/03_2025/8adw_15372.map" model { file = "/net/cci-nas-00/data/ceres_data/8adw_15372/03_2025/8adw_15372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adw_15372/03_2025/8adw_15372.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.86, per 1000 atoms: 0.70 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: 1.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 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: 2.20 Time building geometry restraints manager: 1.95 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.560 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- 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= 0.644 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.001 0.000 HIS D 50 PHE 0.052 0.009 PHE F 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 149 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7128 (mt-10) REVERT: A 98 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6886 (m-30) REVERT: B 92 THR cc_start: 0.8341 (m) cc_final: 0.7941 (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: 0.6964 (m-30) REVERT: E 5 MET cc_start: 0.7329 (ttm) cc_final: 0.7067 (ttt) REVERT: E 12 LYS cc_start: 0.6706 (OUTLIER) cc_final: 0.5540 (pmtt) REVERT: F 5 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7587 (ttt) REVERT: F 28 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: F 98 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.7021 (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: 0.7243 (mp0) REVERT: I 28 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: I 98 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: J 5 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7070 (ttt) 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: 1.2003 time to fit residues: 308.4950 Evaluate side-chains 139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 28 GLU 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 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 75 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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** D 62 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN ** I 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 = 0.4228 r_free = 0.4228 target = 0.146321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.125731 restraints weight = 8863.622| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.27 r_work: 0.3860 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6950 Z= 0.272 Angle : 0.622 4.906 9320 Z= 0.347 Chirality : 0.052 0.128 1160 Planarity : 0.002 0.008 1170 Dihedral : 9.548 57.816 1057 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 7.97 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.015 0.003 PHE H 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 104 time to evaluate : 0.809 Fit side-chains REVERT: A 13 GLU cc_start: 0.7508 (mp0) cc_final: 0.6561 (mm-30) REVERT: A 28 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 98 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: C 5 MET cc_start: 0.8189 (ttm) cc_final: 0.7905 (ttt) REVERT: C 81 THR cc_start: 0.8872 (m) cc_final: 0.8626 (m) REVERT: D 28 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: E 2 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: E 5 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7991 (ttt) REVERT: F 13 GLU cc_start: 0.7478 (mp0) cc_final: 0.6576 (mm-30) REVERT: F 28 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: F 98 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: G 12 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6056 (ttmm) REVERT: H 5 MET cc_start: 0.8189 (ttm) cc_final: 0.7989 (ttt) REVERT: I 28 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: J 2 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: J 10 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8342 (mppt) REVERT: J 20 GLU cc_start: 0.7867 (mp0) cc_final: 0.7613 (mp0) outliers start: 55 outliers final: 18 residues processed: 140 average time/residue: 1.0781 time to fit residues: 159.8564 Evaluate side-chains 121 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 5 MET 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 28 GLU 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 10 LYS 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 26 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 79 optimal weight: 0.0570 chunk 4 optimal weight: 0.0770 chunk 16 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 overall best weight: 1.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4291 r_free = 0.4291 target = 0.150145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.129670 restraints weight = 8976.515| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.27 r_work: 0.3936 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6950 Z= 0.163 Angle : 0.529 4.437 9320 Z= 0.289 Chirality : 0.050 0.129 1160 Planarity : 0.002 0.009 1170 Dihedral : 8.451 59.853 1032 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 6.38 % Allowed : 25.65 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (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 HIS 0.001 0.000 HIS J 50 PHE 0.011 0.002 PHE H 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.780 Fit side-chains REVERT: A 13 GLU cc_start: 0.7201 (mp0) cc_final: 0.6512 (mm-30) REVERT: A 28 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: C 5 MET cc_start: 0.8219 (ttm) cc_final: 0.7952 (ttt) REVERT: C 81 THR cc_start: 0.8719 (m) cc_final: 0.8510 (m) REVERT: E 2 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: E 5 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8097 (ttt) REVERT: E 20 GLU cc_start: 0.7943 (mp0) cc_final: 0.7738 (pm20) REVERT: F 12 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6082 (tppt) REVERT: F 13 GLU cc_start: 0.7179 (mp0) cc_final: 0.6788 (mm-30) REVERT: F 28 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: G 83 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7095 (mm-30) REVERT: H 5 MET cc_start: 0.8252 (ttm) cc_final: 0.8043 (ttt) REVERT: J 2 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: J 5 MET cc_start: 0.8353 (ttp) cc_final: 0.8117 (ttt) REVERT: J 20 GLU cc_start: 0.7894 (mp0) cc_final: 0.7689 (mp0) outliers start: 44 outliers final: 21 residues processed: 148 average time/residue: 1.1100 time to fit residues: 173.9044 Evaluate side-chains 135 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 B residue 59 THR 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 5 MET 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 28 GLU 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 59 THR Chi-restraints excluded: chain G residue 83 GLU 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 63 VAL Chi-restraints excluded: chain J residue 2 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 6.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 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 = 0.4134 r_free = 0.4134 target = 0.138875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118506 restraints weight = 9256.333| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.26 r_work: 0.3770 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 6950 Z= 0.492 Angle : 0.694 4.595 9320 Z= 0.388 Chirality : 0.054 0.137 1160 Planarity : 0.003 0.016 1170 Dihedral : 9.287 79.497 1024 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 7.97 % Allowed : 25.51 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.017 0.004 PHE I 4 TYR 0.009 0.003 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 114 time to evaluate : 0.838 Fit side-chains REVERT: A 13 GLU cc_start: 0.7575 (mp0) cc_final: 0.6758 (tp30) REVERT: A 28 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: C 5 MET cc_start: 0.8296 (ttm) cc_final: 0.7953 (ttt) REVERT: C 98 ASP cc_start: 0.7249 (m-30) cc_final: 0.7010 (m-30) REVERT: E 2 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6922 (p0) REVERT: F 12 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.5903 (tppt) REVERT: F 13 GLU cc_start: 0.7608 (mp0) cc_final: 0.7215 (tp30) REVERT: G 58 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8210 (tmtm) REVERT: G 83 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: H 5 MET cc_start: 0.8231 (ttm) cc_final: 0.7960 (ttt) REVERT: H 98 ASP cc_start: 0.7281 (m-30) cc_final: 0.7078 (m-30) REVERT: I 83 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6267 (mm-30) REVERT: J 2 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.6996 (p0) outliers start: 55 outliers final: 23 residues processed: 147 average time/residue: 1.0933 time to fit residues: 169.6495 Evaluate side-chains 145 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 12 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 83 GLU 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 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 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 34 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.4201 r_free = 0.4201 target = 0.143389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.123184 restraints weight = 9080.482| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.22 r_work: 0.3836 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3200 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= 0.303 Angle : 0.615 5.857 9320 Z= 0.337 Chirality : 0.052 0.135 1160 Planarity : 0.002 0.014 1170 Dihedral : 7.802 54.977 1017 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.96 % Allowed : 27.97 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.012 0.003 PHE H 94 TYR 0.006 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.757 Fit side-chains REVERT: A 13 GLU cc_start: 0.7484 (mp0) cc_final: 0.6727 (tp30) REVERT: B 58 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8055 (tmtm) REVERT: C 5 MET cc_start: 0.8242 (ttm) cc_final: 0.7985 (ttt) REVERT: C 98 ASP cc_start: 0.7368 (m-30) cc_final: 0.7103 (m-30) REVERT: E 2 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6979 (p0) REVERT: E 5 MET cc_start: 0.8459 (ttp) cc_final: 0.8190 (ttt) REVERT: F 12 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6012 (tppt) REVERT: F 13 GLU cc_start: 0.7505 (mp0) cc_final: 0.7179 (tp30) REVERT: G 58 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8126 (tmtm) REVERT: J 2 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6789 (p0) REVERT: J 5 MET cc_start: 0.8451 (ttp) cc_final: 0.8174 (ttt) REVERT: J 10 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8660 (mppt) outliers start: 48 outliers final: 22 residues processed: 160 average time/residue: 1.0442 time to fit residues: 176.8442 Evaluate side-chains 147 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain B residue 59 THR 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 12 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 LYS 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 J residue 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.4206 r_free = 0.4206 target = 0.143160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.123212 restraints weight = 9093.696| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.18 r_work: 0.3858 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6950 Z= 0.273 Angle : 0.609 6.464 9320 Z= 0.333 Chirality : 0.051 0.135 1160 Planarity : 0.002 0.015 1170 Dihedral : 6.893 51.102 1010 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 6.81 % Allowed : 29.28 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (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 HIS 0.001 0.001 HIS G 50 PHE 0.012 0.003 PHE H 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.860 Fit side-chains REVERT: A 13 GLU cc_start: 0.7476 (mp0) cc_final: 0.6730 (tp30) REVERT: B 46 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 58 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8045 (tmtm) REVERT: C 5 MET cc_start: 0.8278 (ttm) cc_final: 0.7995 (ttt) REVERT: D 2 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: E 2 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7113 (p0) REVERT: E 5 MET cc_start: 0.8448 (ttp) cc_final: 0.8187 (ttt) REVERT: E 83 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: F 13 GLU cc_start: 0.7481 (mp0) cc_final: 0.6790 (tp30) REVERT: G 58 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8081 (tmtm) REVERT: I 2 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7476 (m-30) REVERT: I 83 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6308 (mm-30) REVERT: J 2 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6769 (p0) REVERT: J 5 MET cc_start: 0.8403 (ttp) cc_final: 0.8143 (ttt) REVERT: J 10 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8686 (mppt) outliers start: 47 outliers final: 20 residues processed: 162 average time/residue: 1.0729 time to fit residues: 183.8287 Evaluate side-chains 156 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain B residue 59 THR 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 83 GLU 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 58 LYS Chi-restraints excluded: chain G residue 59 THR 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 10 LYS 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 15 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.4237 r_free = 0.4237 target = 0.145328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.125518 restraints weight = 8936.700| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.15 r_work: 0.3883 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6950 Z= 0.246 Angle : 0.608 7.225 9320 Z= 0.330 Chirality : 0.051 0.134 1160 Planarity : 0.002 0.015 1170 Dihedral : 6.600 51.347 1010 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.36 % Allowed : 30.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.017 0.003 PHE E 4 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.668 Fit side-chains REVERT: A 13 GLU cc_start: 0.7495 (mp0) cc_final: 0.6720 (tp30) REVERT: B 46 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7853 (mt-10) REVERT: B 58 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8026 (tmtm) REVERT: B 61 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 5 MET cc_start: 0.8253 (ttm) cc_final: 0.7970 (ttt) REVERT: D 2 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: E 5 MET cc_start: 0.8412 (ttp) cc_final: 0.8148 (ttt) REVERT: E 20 GLU cc_start: 0.7897 (mp0) cc_final: 0.7680 (pm20) REVERT: F 13 GLU cc_start: 0.7490 (mp0) cc_final: 0.6733 (mm-30) REVERT: G 58 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (tmtm) REVERT: I 2 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: I 83 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6278 (mm-30) REVERT: J 2 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6971 (p0) REVERT: J 5 MET cc_start: 0.8448 (ttp) cc_final: 0.8144 (ttt) REVERT: J 10 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8663 (mppt) REVERT: J 20 GLU cc_start: 0.7931 (mp0) cc_final: 0.7682 (pm20) outliers start: 37 outliers final: 20 residues processed: 154 average time/residue: 1.0930 time to fit residues: 177.9487 Evaluate side-chains 156 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain B residue 59 THR 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 72 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 9 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 59 THR 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 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 LYS 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 71 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 86 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** I 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 = 0.4214 r_free = 0.4214 target = 0.143162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123543 restraints weight = 9367.441| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.27 r_work: 0.3851 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6950 Z= 0.271 Angle : 0.625 7.159 9320 Z= 0.340 Chirality : 0.051 0.135 1160 Planarity : 0.002 0.016 1170 Dihedral : 6.475 51.539 1008 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.36 % Allowed : 31.74 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.019 0.003 PHE E 4 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.804 Fit side-chains REVERT: A 13 GLU cc_start: 0.7490 (mp0) cc_final: 0.6725 (mm-30) REVERT: B 58 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7961 (tmtm) REVERT: C 5 MET cc_start: 0.8218 (ttm) cc_final: 0.7906 (ttt) REVERT: E 1 MET cc_start: 0.4482 (tmm) cc_final: 0.4203 (tmm) REVERT: E 5 MET cc_start: 0.8385 (ttp) cc_final: 0.8085 (ttt) REVERT: E 61 GLU cc_start: 0.7551 (tp30) cc_final: 0.7173 (tp30) REVERT: E 83 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: F 13 GLU cc_start: 0.7387 (mp0) cc_final: 0.6670 (mm-30) REVERT: G 58 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8019 (tmtm) REVERT: I 2 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7401 (m-30) REVERT: I 5 MET cc_start: 0.8549 (ttp) cc_final: 0.8310 (ptm) REVERT: I 83 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6270 (mm-30) REVERT: J 2 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.7036 (p0) REVERT: J 5 MET cc_start: 0.8428 (ttp) cc_final: 0.8132 (ttt) REVERT: J 10 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8689 (mppt) outliers start: 37 outliers final: 19 residues processed: 154 average time/residue: 1.0905 time to fit residues: 177.7666 Evaluate side-chains 155 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain B residue 59 THR 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 72 THR Chi-restraints excluded: chain E residue 83 GLU 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 58 LYS Chi-restraints excluded: chain G residue 59 THR 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 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 LYS 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 53 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** I 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 = 0.4205 r_free = 0.4205 target = 0.142365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.123115 restraints weight = 9421.037| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.18 r_work: 0.3849 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6950 Z= 0.297 Angle : 0.660 7.564 9320 Z= 0.357 Chirality : 0.052 0.143 1160 Planarity : 0.002 0.017 1170 Dihedral : 6.472 52.540 1006 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.93 % Allowed : 32.46 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 50 PHE 0.020 0.003 PHE E 4 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.772 Fit side-chains REVERT: A 13 GLU cc_start: 0.7322 (mp0) cc_final: 0.6645 (mm-30) REVERT: A 46 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: B 13 GLU cc_start: 0.7901 (mp0) cc_final: 0.7693 (pm20) REVERT: B 58 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (tmtm) REVERT: B 79 GLN cc_start: 0.7133 (tm-30) cc_final: 0.6550 (tm-30) REVERT: C 5 MET cc_start: 0.8176 (ttm) cc_final: 0.7920 (ttt) REVERT: E 1 MET cc_start: 0.4641 (tmm) cc_final: 0.4364 (tmm) REVERT: E 5 MET cc_start: 0.8483 (ttp) cc_final: 0.8229 (ttt) REVERT: E 20 GLU cc_start: 0.7931 (mp0) cc_final: 0.7720 (mp0) REVERT: E 83 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: F 13 GLU cc_start: 0.7377 (mp0) cc_final: 0.6782 (mm-30) REVERT: G 58 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8069 (tmtm) REVERT: I 2 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: I 5 MET cc_start: 0.8587 (ttp) cc_final: 0.8383 (ptm) REVERT: I 83 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6301 (mm-30) REVERT: J 1 MET cc_start: 0.5029 (tmm) cc_final: 0.4800 (tmm) REVERT: J 2 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7088 (p0) REVERT: J 5 MET cc_start: 0.8433 (ttp) cc_final: 0.8144 (ttt) REVERT: J 10 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8681 (mppt) outliers start: 34 outliers final: 20 residues processed: 151 average time/residue: 0.9990 time to fit residues: 160.4658 Evaluate side-chains 156 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 59 THR 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 E residue 83 GLU 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 58 LYS 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 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 LYS 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 83 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** I 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 = 0.4130 r_free = 0.4130 target = 0.137517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.117968 restraints weight = 9642.499| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.25 r_work: 0.3764 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 6950 Z= 0.515 Angle : 0.762 7.116 9320 Z= 0.417 Chirality : 0.055 0.188 1160 Planarity : 0.003 0.017 1170 Dihedral : 7.210 54.446 1006 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.93 % Allowed : 32.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.031 0.005 PHE E 4 TYR 0.008 0.002 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.740 Fit side-chains REVERT: A 13 GLU cc_start: 0.7384 (mp0) cc_final: 0.6707 (tp30) REVERT: B 58 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8104 (tmtm) REVERT: B 79 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6643 (tm-30) REVERT: E 5 MET cc_start: 0.8448 (ttp) cc_final: 0.8195 (ttt) REVERT: E 83 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: F 13 GLU cc_start: 0.7405 (mp0) cc_final: 0.6673 (tp30) REVERT: G 58 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8090 (tmtm) REVERT: I 2 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: I 5 MET cc_start: 0.8574 (ttp) cc_final: 0.8340 (ptm) REVERT: I 83 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6259 (mm-30) REVERT: J 2 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7047 (p0) REVERT: J 5 MET cc_start: 0.8378 (ttp) cc_final: 0.8096 (ttt) REVERT: J 10 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8581 (mppt) REVERT: J 20 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8132 (pm20) outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 1.0903 time to fit residues: 176.3100 Evaluate side-chains 154 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 58 LYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 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 E residue 83 GLU 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 58 LYS 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 2 ASP Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 20 GLU 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 50 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.4261 r_free = 0.4261 target = 0.146413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.127091 restraints weight = 9250.508| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.18 r_work: 0.3911 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6950 Z= 0.214 Angle : 0.644 7.019 9320 Z= 0.344 Chirality : 0.051 0.134 1160 Planarity : 0.002 0.018 1170 Dihedral : 6.219 56.345 1006 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.48 % Allowed : 35.36 % Favored : 61.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.012 0.003 PHE E 4 TYR 0.009 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.54 seconds wall clock time: 91 minutes 29.99 seconds (5489.99 seconds total)