Starting phenix.real_space_refine on Fri Dec 27 22:09:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adw_15372/12_2024/8adw_15372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adw_15372/12_2024/8adw_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_15372/12_2024/8adw_15372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adw_15372/12_2024/8adw_15372.map" model { file = "/net/cci-nas-00/data/ceres_data/8adw_15372/12_2024/8adw_15372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adw_15372/12_2024/8adw_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-5532/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: 4.65, per 1000 atoms: 0.67 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: 1.66 Conformation dependent library (CDL) restraints added in 1.0 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: 1.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.745A pdb=" N PHE A 4 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 4 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE C 4 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE D 4 " --> pdb=" O MET E 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.246A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA B 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA C 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA E 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 32 removed outlier: 6.361A pdb=" N ALA A 27 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA B 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 29 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY A 31 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 27 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA C 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 31 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 27 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA D 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 29 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS D 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY C 31 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA E 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA D 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS E 32 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY D 31 " --> pdb=" O LYS E 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 35 through 40 removed outlier: 6.740A pdb=" N GLY B 36 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 36 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY D 36 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY E 36 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 70 through 71 removed outlier: 6.280A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 74 through 78 Processing sheet with id=AB1, first strand: chain 'A' and resid 87 through 95 removed outlier: 6.098A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA B 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL B 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA C 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA B 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY C 93 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR B 92 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL C 95 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE B 94 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA D 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL D 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 91 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA D 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLY E 93 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N VAL E 95 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.752A pdb=" N PHE F 4 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE G 4 " --> pdb=" O MET H 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE H 4 " --> pdb=" O MET I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE I 4 " --> pdb=" O MET J 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 15 through 20 removed outlier: 6.249A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA G 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA H 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA G 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU H 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA G 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA H 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU I 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'F' and resid 27 through 32 removed outlier: 6.361A pdb=" N ALA F 27 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA G 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA F 29 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS G 32 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY F 31 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA G 27 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA H 30 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA G 29 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LYS H 32 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY G 31 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA H 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA I 30 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA H 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS I 32 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY H 31 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA I 27 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 30 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA I 29 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N LYS J 32 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 6.739A pdb=" N GLY G 36 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY H 36 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY I 36 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY J 36 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 48 through 55 Processing sheet with id=AB8, first strand: chain 'F' and resid 61 through 66 Processing sheet with id=AB9, first strand: chain 'F' and resid 70 through 71 removed outlier: 6.274A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL G 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 74 through 77 removed outlier: 6.237A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL H 74 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL I 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA H 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL I 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL J 77 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 83 removed outlier: 6.609A pdb=" N VAL F 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL H 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL I 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 95 removed outlier: 6.093A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA G 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL G 95 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE F 94 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE G 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA H 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA G 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY H 93 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR G 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL H 95 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE G 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE H 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA I 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA H 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY I 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR H 92 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 10.741A pdb=" N VAL I 95 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE H 94 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE I 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA J 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N VAL J 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N PHE I 94 " --> pdb=" O VAL J 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 152 hydrogen bonds defined for protein. 456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.90 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.690 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 : 0.973 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: 1.1786 time to fit residues: 303.5100 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 : 0.819 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.836 Fit side-chains REVERT: A 13 GLU cc_start: 0.6953 (mp0) cc_final: 0.6279 (mm-30) REVERT: A 28 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 98 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: C 5 MET cc_start: 0.7499 (ttm) cc_final: 0.7256 (ttt) REVERT: C 81 THR cc_start: 0.8712 (m) cc_final: 0.8462 (m) REVERT: D 28 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: E 2 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6655 (m-30) REVERT: E 5 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7322 (ttt) REVERT: F 13 GLU cc_start: 0.6897 (mp0) cc_final: 0.6247 (mm-30) REVERT: F 28 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: F 98 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: G 12 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5964 (ttmm) REVERT: I 28 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: J 2 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: J 10 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8307 (mppt) outliers start: 55 outliers final: 18 residues processed: 140 average time/residue: 1.0875 time to fit residues: 161.3378 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 : 0.807 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 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** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 6950 Z= 0.498 Angle : 0.703 4.317 9320 Z= 0.395 Chirality : 0.054 0.134 1160 Planarity : 0.003 0.010 1170 Dihedral : 9.717 59.861 1032 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 9.13 % Allowed : 23.91 % Favored : 66.96 % 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: -3.62 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.016 0.004 PHE H 4 TYR 0.011 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 116 time to evaluate : 0.788 Fit side-chains REVERT: B 5 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7392 (ttp) REVERT: B 12 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6083 (ttmm) REVERT: B 58 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8015 (tmtm) REVERT: C 5 MET cc_start: 0.7541 (ttm) cc_final: 0.7268 (ttt) REVERT: C 13 GLU cc_start: 0.7561 (mp0) cc_final: 0.7312 (mp0) REVERT: C 98 ASP cc_start: 0.7594 (m-30) cc_final: 0.7301 (m-30) REVERT: D 28 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: D 98 ASP cc_start: 0.7738 (p0) cc_final: 0.7499 (p0) REVERT: E 2 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: F 12 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6160 (tppt) REVERT: F 28 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: G 12 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5936 (ttmm) REVERT: G 58 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8061 (tmtm) REVERT: H 98 ASP cc_start: 0.7657 (m-30) cc_final: 0.7354 (m-30) REVERT: I 5 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7523 (ttp) REVERT: I 98 ASP cc_start: 0.7754 (p0) cc_final: 0.7532 (p0) REVERT: J 2 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6605 (m-30) outliers start: 63 outliers final: 23 residues processed: 157 average time/residue: 1.1419 time to fit residues: 189.1214 Evaluate side-chains 145 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 A residue 98 ASP Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 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 G residue 58 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6950 Z= 0.260 Angle : 0.589 6.813 9320 Z= 0.321 Chirality : 0.051 0.133 1160 Planarity : 0.002 0.012 1170 Dihedral : 8.647 59.607 1026 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 6.67 % Allowed : 28.12 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.43 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.17), 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 B 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 167 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6488 (mp0) cc_final: 0.6076 (tp30) REVERT: B 12 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5979 (ttmm) REVERT: B 58 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7914 (tmtm) REVERT: C 98 ASP cc_start: 0.7445 (m-30) cc_final: 0.6994 (m-30) REVERT: D 98 ASP cc_start: 0.7520 (p0) cc_final: 0.7260 (p0) REVERT: E 5 MET cc_start: 0.7774 (ttp) cc_final: 0.7504 (ttt) REVERT: F 12 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6248 (tppt) REVERT: G 12 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6153 (ttmm) REVERT: H 2 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6778 (m-30) REVERT: H 98 ASP cc_start: 0.7526 (m-30) cc_final: 0.7031 (m-30) REVERT: I 83 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6167 (mm-30) REVERT: I 98 ASP cc_start: 0.7534 (p0) cc_final: 0.7285 (p0) REVERT: J 5 MET cc_start: 0.7767 (ttp) cc_final: 0.7513 (ttt) REVERT: J 10 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8601 (mppt) outliers start: 46 outliers final: 22 residues processed: 155 average time/residue: 1.0615 time to fit residues: 174.5492 Evaluate side-chains 145 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain 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 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 6950 Z= 0.412 Angle : 0.666 7.643 9320 Z= 0.368 Chirality : 0.053 0.138 1160 Planarity : 0.003 0.016 1170 Dihedral : 8.179 58.990 1016 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 7.10 % Allowed : 28.12 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.49 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.014 0.004 PHE D 4 TYR 0.010 0.002 TYR A 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 174 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.858 Fit side-chains REVERT: A 13 GLU cc_start: 0.6595 (mp0) cc_final: 0.6025 (tp30) REVERT: B 12 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.5816 (ttmm) REVERT: B 58 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7940 (tmtm) REVERT: C 2 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6742 (m-30) REVERT: C 38 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8847 (tp) REVERT: C 98 ASP cc_start: 0.7798 (m-30) cc_final: 0.7243 (m-30) REVERT: D 2 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: D 98 ASP cc_start: 0.7637 (p0) cc_final: 0.7379 (p0) REVERT: E 5 MET cc_start: 0.7710 (ttp) cc_final: 0.7430 (ttt) REVERT: G 12 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6102 (ttmm) REVERT: G 58 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8033 (tmtm) REVERT: H 2 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: H 38 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8862 (tp) REVERT: H 98 ASP cc_start: 0.7715 (m-30) cc_final: 0.7158 (m-30) REVERT: I 83 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6254 (mt-10) REVERT: I 98 ASP cc_start: 0.7613 (p0) cc_final: 0.7378 (p0) REVERT: J 2 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: J 5 MET cc_start: 0.7837 (ttp) cc_final: 0.7570 (ttt) REVERT: J 10 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8690 (mppt) outliers start: 49 outliers final: 18 residues processed: 157 average time/residue: 1.2559 time to fit residues: 208.1851 Evaluate side-chains 148 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 38 LEU 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 10 LYS Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN F 99 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6950 Z= 0.283 Angle : 0.614 6.864 9320 Z= 0.333 Chirality : 0.051 0.135 1160 Planarity : 0.002 0.014 1170 Dihedral : 7.819 57.119 1016 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.67 % Allowed : 28.84 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS G 50 PHE 0.013 0.003 PHE C 94 TYR 0.008 0.002 TYR A 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 178 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.825 Fit side-chains REVERT: A 13 GLU cc_start: 0.6414 (mp0) cc_final: 0.5962 (tp30) REVERT: B 12 LYS cc_start: 0.6435 (OUTLIER) cc_final: 0.5838 (ttmm) REVERT: B 58 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7942 (tmtm) REVERT: B 61 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6952 (tp30) REVERT: C 2 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: C 38 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8901 (tp) REVERT: C 98 ASP cc_start: 0.7766 (m-30) cc_final: 0.7195 (m-30) REVERT: D 2 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: D 98 ASP cc_start: 0.7542 (p0) cc_final: 0.7216 (p0) REVERT: E 2 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6769 (p0) REVERT: E 5 MET cc_start: 0.7680 (ttp) cc_final: 0.7406 (ttt) REVERT: G 58 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7977 (tmtm) REVERT: H 2 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6803 (m-30) REVERT: H 38 LEU cc_start: 0.9112 (tp) cc_final: 0.8893 (tp) REVERT: H 98 ASP cc_start: 0.7668 (m-30) cc_final: 0.7220 (m-30) REVERT: I 83 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: I 98 ASP cc_start: 0.7463 (p0) cc_final: 0.7164 (p0) REVERT: J 2 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: J 5 MET cc_start: 0.7836 (ttp) cc_final: 0.7584 (ttt) REVERT: J 10 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8711 (mppt) outliers start: 46 outliers final: 20 residues processed: 160 average time/residue: 1.0902 time to fit residues: 185.0978 Evaluate side-chains 155 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 38 LEU 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 2 ASP Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 83 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 86 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6950 Z= 0.210 Angle : 0.587 6.725 9320 Z= 0.315 Chirality : 0.051 0.133 1160 Planarity : 0.002 0.014 1170 Dihedral : 7.427 57.715 1016 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.09 % Allowed : 29.86 % 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: -3.32 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.012 0.003 PHE H 94 TYR 0.007 0.002 TYR F 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 170 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.737 Fit side-chains REVERT: A 13 GLU cc_start: 0.6219 (mp0) cc_final: 0.5814 (tp30) REVERT: A 46 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6539 (mm-30) REVERT: B 12 LYS cc_start: 0.6419 (OUTLIER) cc_final: 0.5866 (ttmm) REVERT: B 58 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7890 (tmtm) REVERT: C 2 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: C 38 LEU cc_start: 0.9084 (tp) cc_final: 0.8878 (tp) REVERT: C 98 ASP cc_start: 0.7831 (m-30) cc_final: 0.7228 (m-30) REVERT: D 2 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: D 80 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7524 (mttt) REVERT: D 98 ASP cc_start: 0.7471 (p0) cc_final: 0.7220 (p0) REVERT: E 2 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6778 (p0) REVERT: E 5 MET cc_start: 0.7706 (ttp) cc_final: 0.7450 (ttt) REVERT: G 58 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7976 (tmtm) REVERT: H 2 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: H 98 ASP cc_start: 0.7650 (m-30) cc_final: 0.7171 (m-30) REVERT: J 2 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: J 5 MET cc_start: 0.7857 (ttp) cc_final: 0.7634 (ttt) REVERT: J 20 GLU cc_start: 0.7617 (mp0) cc_final: 0.7345 (pm20) outliers start: 42 outliers final: 17 residues processed: 156 average time/residue: 1.1163 time to fit residues: 184.3815 Evaluate side-chains 149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 2 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6950 Z= 0.383 Angle : 0.680 6.801 9320 Z= 0.371 Chirality : 0.052 0.152 1160 Planarity : 0.003 0.017 1170 Dihedral : 7.779 59.657 1014 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.65 % Allowed : 31.01 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (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 0.002 0.001 HIS G 50 PHE 0.013 0.004 PHE C 94 TYR 0.015 0.002 TYR A 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 167 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.835 Fit side-chains REVERT: A 13 GLU cc_start: 0.6360 (mp0) cc_final: 0.5854 (tp30) REVERT: B 12 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5749 (ttmm) REVERT: B 13 GLU cc_start: 0.7764 (mp0) cc_final: 0.7417 (mp0) REVERT: B 58 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7945 (tmtm) REVERT: C 38 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8858 (tp) REVERT: C 98 ASP cc_start: 0.7953 (m-30) cc_final: 0.7377 (m-30) REVERT: D 2 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: D 80 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7693 (mttt) REVERT: D 98 ASP cc_start: 0.7596 (p0) cc_final: 0.7279 (p0) REVERT: E 2 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6921 (p0) REVERT: E 5 MET cc_start: 0.7743 (ttp) cc_final: 0.7448 (ttt) REVERT: F 46 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: G 58 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8019 (tmtm) REVERT: H 2 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: I 98 ASP cc_start: 0.7219 (p0) cc_final: 0.7009 (p0) REVERT: J 2 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: J 5 MET cc_start: 0.7898 (ttp) cc_final: 0.7644 (ttt) outliers start: 39 outliers final: 16 residues processed: 151 average time/residue: 1.0508 time to fit residues: 168.1190 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 : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 38 LEU 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 80 LYS 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 F residue 2 ASP Chi-restraints excluded: chain F residue 46 GLU 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 2 ASP 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 J residue 2 ASP 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 80 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6950 Z= 0.219 Angle : 0.637 7.498 9320 Z= 0.339 Chirality : 0.051 0.132 1160 Planarity : 0.002 0.013 1170 Dihedral : 7.293 59.180 1014 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.06 % Allowed : 33.19 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.29 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.013 0.003 PHE E 4 TYR 0.012 0.002 TYR A 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 158 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6253 (mp0) cc_final: 0.5817 (tp30) REVERT: B 58 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7913 (tmtm) REVERT: B 79 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6339 (tm-30) REVERT: C 2 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: C 38 LEU cc_start: 0.9075 (tp) cc_final: 0.8862 (tp) REVERT: C 98 ASP cc_start: 0.7879 (m-30) cc_final: 0.7297 (m-30) REVERT: E 5 MET cc_start: 0.7692 (ttp) cc_final: 0.7401 (ttt) REVERT: F 46 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: G 58 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7899 (tmtm) REVERT: H 2 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: I 83 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6239 (mm-30) REVERT: J 5 MET cc_start: 0.7856 (ttp) cc_final: 0.7620 (ttt) REVERT: J 20 GLU cc_start: 0.7655 (mp0) cc_final: 0.7411 (pm20) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 1.1388 time to fit residues: 181.8161 Evaluate side-chains 149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 12 LYS 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 2 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 2 ASP Chi-restraints excluded: chain F residue 46 GLU 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 2 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 71 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6950 Z= 0.398 Angle : 0.716 6.972 9320 Z= 0.388 Chirality : 0.053 0.164 1160 Planarity : 0.003 0.013 1170 Dihedral : 7.458 55.918 1010 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.48 % Allowed : 34.35 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.39 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.027 0.004 PHE E 4 TYR 0.016 0.002 TYR F 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 158 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.890 Fit side-chains REVERT: A 13 GLU cc_start: 0.6316 (mp0) cc_final: 0.5880 (tp30) REVERT: B 58 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7946 (tmtm) REVERT: B 79 GLN cc_start: 0.6805 (tm-30) cc_final: 0.6269 (tm-30) REVERT: C 38 LEU cc_start: 0.9081 (tp) cc_final: 0.8868 (tp) REVERT: E 5 MET cc_start: 0.7722 (ttp) cc_final: 0.7445 (ttt) REVERT: F 46 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: G 58 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8033 (tmtm) REVERT: H 2 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: I 83 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6284 (mm-30) REVERT: J 2 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6737 (m-30) REVERT: J 5 MET cc_start: 0.7913 (ttp) cc_final: 0.7681 (ttt) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 1.1086 time to fit residues: 178.1501 Evaluate side-chains 151 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 58 LYS 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 F residue 2 ASP Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 2 ASP Chi-restraints excluded: chain G residue 58 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 59 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 2 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 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 = 0.4137 r_free = 0.4137 target = 0.137753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.118391 restraints weight = 9403.031| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.16 r_work: 0.3772 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3712 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= 0.476 Angle : 0.765 6.793 9320 Z= 0.414 Chirality : 0.054 0.176 1160 Planarity : 0.003 0.016 1170 Dihedral : 7.596 59.396 1008 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.91 % Allowed : 34.35 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.027 0.004 PHE E 4 TYR 0.020 0.003 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.53 seconds wall clock time: 58 minutes 36.06 seconds (3516.06 seconds total)