Starting phenix.real_space_refine on Sun Mar 10 19:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osj_20183/03_2024/6osj_20183.pdb" } resolution = 2.8 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= 0.000 sd= 0.009 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: 3 Type Number sf(0) Gaussians C 2650 2.51 5 N 730 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4210 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "H" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "I" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "J" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 2.49, per 1000 atoms: 0.59 Number of scatterers: 4210 At special positions: 0 Unit cell: (92.22, 75.26, 40.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 830 8.00 N 730 7.00 C 2650 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 - 3.50 Amino acid : False - 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: 1.26 Conformation dependent library (CDL) restraints added in 745.9 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.687A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 58 removed outlier: 6.572A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.828A pdb=" N VAL A 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY C 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN C 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL C 70 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL E 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 72 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ALA C 78 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN E 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS C 80 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL E 70 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR E 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY G 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA E 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLN G 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS E 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR G 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL E 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL G 70 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL I 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR G 72 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY I 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL I 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA G 78 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN I 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS G 80 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR I 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 82 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 90 removed outlier: 6.490A pdb=" N ALA A 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.625A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 58 removed outlier: 6.627A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 82 removed outlier: 6.935A pdb=" N VAL B 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY D 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS B 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR D 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL B 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL D 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY F 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLN F 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS D 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR F 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL D 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL F 70 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR F 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY H 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA F 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN H 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS F 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR H 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL F 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL H 70 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL J 71 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR H 72 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY J 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL J 77 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA H 78 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN J 79 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS H 80 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR J 81 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL H 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.464A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA F 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 29 hydrogen bonds defined for protein. 87 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 720 1.29 - 1.35: 660 1.35 - 1.42: 170 1.42 - 1.48: 781 1.48 - 1.55: 1899 Bond restraints: 4230 Sorted by residual: bond pdb=" CA ALA F 89 " pdb=" CB ALA F 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.33e+00 bond pdb=" CA ALA C 89 " pdb=" CB ALA C 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.29e+00 bond pdb=" CA ALA D 89 " pdb=" CB ALA D 89 " ideal model delta sigma weight residual 1.531 1.466 0.065 3.12e-02 1.03e+03 4.29e+00 bond pdb=" CA ALA I 89 " pdb=" CB ALA I 89 " ideal model delta sigma weight residual 1.531 1.466 0.064 3.12e-02 1.03e+03 4.27e+00 bond pdb=" CA ALA B 89 " pdb=" CB ALA B 89 " ideal model delta sigma weight residual 1.531 1.466 0.064 3.12e-02 1.03e+03 4.23e+00 ... (remaining 4225 not shown) Histogram of bond angle deviations from ideal: 105.69 - 110.72: 1629 110.72 - 115.76: 1379 115.76 - 120.80: 1279 120.80 - 125.83: 1393 125.83 - 130.87: 40 Bond angle restraints: 5720 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.41 112.57 8.84 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 121.41 112.58 8.83 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 121.41 112.58 8.83 1.83e+00 2.99e-01 2.33e+01 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.41 112.59 8.82 1.83e+00 2.99e-01 2.32e+01 angle pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta sigma weight residual 121.41 112.59 8.82 1.83e+00 2.99e-01 2.32e+01 ... (remaining 5715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 2170 13.29 - 26.57: 220 26.57 - 39.85: 40 39.85 - 53.14: 20 53.14 - 66.42: 20 Dihedral angle restraints: 2470 sinusoidal: 820 harmonic: 1650 Sorted by residual: dihedral pdb=" CA GLY F 51 " pdb=" C GLY F 51 " pdb=" N VAL F 52 " pdb=" CA VAL F 52 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLY H 51 " pdb=" C GLY H 51 " pdb=" N VAL H 52 " pdb=" CA VAL H 52 " ideal model delta harmonic sigma weight residual -180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLY C 51 " pdb=" C GLY C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 2467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 533 0.064 - 0.128: 187 0.128 - 0.192: 20 0.192 - 0.256: 10 0.256 - 0.320: 10 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS I 50 " pdb=" N HIS I 50 " pdb=" C HIS I 50 " pdb=" CB HIS I 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA HIS G 50 " pdb=" N HIS G 50 " pdb=" C HIS G 50 " pdb=" CB HIS G 50 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 757 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.020 2.00e-02 2.50e+03 1.09e-02 2.37e+00 pdb=" CG TYR A 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " 0.020 2.00e-02 2.50e+03 1.08e-02 2.35e+00 pdb=" CG TYR F 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 39 " 0.019 2.00e-02 2.50e+03 1.07e-02 2.29e+00 pdb=" CG TYR E 39 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR E 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 39 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 39 " 0.006 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 712 2.76 - 3.30: 3943 3.30 - 3.83: 6750 3.83 - 4.37: 7647 4.37 - 4.90: 15935 Nonbonded interactions: 34987 Sorted by model distance: nonbonded pdb=" OE2 GLU F 57 " pdb=" ND1 HIS G 50 " model vdw 2.227 2.520 nonbonded pdb=" OE2 GLU D 57 " pdb=" ND1 HIS E 50 " model vdw 2.258 2.520 nonbonded pdb=" OE2 GLU H 57 " pdb=" ND1 HIS I 50 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU B 57 " pdb=" ND1 HIS C 50 " model vdw 2.264 2.520 nonbonded pdb=" O SER A 42 " pdb=" OG1 THR A 44 " model vdw 2.329 2.440 ... (remaining 34982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.310 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: 1.790 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.340 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.011 0.065 4230 Z= 0.772 Angle : 1.127 8.838 5720 Z= 0.666 Chirality : 0.072 0.320 760 Planarity : 0.004 0.012 700 Dihedral : 13.688 66.424 1430 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Rotamer: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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: -4.71 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.008 HIS B 50 PHE 0.010 0.003 PHE D 94 TYR 0.022 0.007 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.506 Fit side-chains REVERT: D 83 GLU cc_start: 0.7176 (tt0) cc_final: 0.6916 (mt-10) REVERT: F 60 LYS cc_start: 0.7751 (mttt) cc_final: 0.7485 (ttmm) REVERT: F 65 ASN cc_start: 0.8171 (t0) cc_final: 0.7954 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.1654 time to fit residues: 60.8618 Evaluate side-chains 37 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN H 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4230 Z= 0.393 Angle : 0.896 8.367 5720 Z= 0.521 Chirality : 0.064 0.303 760 Planarity : 0.003 0.016 700 Dihedral : 6.512 19.620 610 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % Rotamer: Outliers : 5.58 % Allowed : 14.19 % Favored : 80.23 % 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: -4.47 (0.28), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.011 0.002 PHE F 94 TYR 0.020 0.005 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.481 Fit side-chains REVERT: A 54 THR cc_start: 0.8304 (p) cc_final: 0.8066 (m) REVERT: C 38 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6490 (mm) REVERT: C 54 THR cc_start: 0.8595 (p) cc_final: 0.8246 (m) REVERT: C 97 LYS cc_start: 0.7390 (mtpt) cc_final: 0.7028 (mttm) REVERT: D 54 THR cc_start: 0.8664 (p) cc_final: 0.8114 (m) REVERT: G 38 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6597 (tp) REVERT: J 83 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6727 (tt0) outliers start: 24 outliers final: 11 residues processed: 68 average time/residue: 0.7915 time to fit residues: 56.8851 Evaluate side-chains 55 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4230 Z= 0.459 Angle : 0.948 8.797 5720 Z= 0.551 Chirality : 0.066 0.316 760 Planarity : 0.004 0.014 700 Dihedral : 6.604 19.388 610 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.85 % Favored : 79.15 % Rotamer: Outliers : 7.21 % Allowed : 15.12 % Favored : 77.67 % 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: -4.36 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.013 0.003 PHE F 94 TYR 0.020 0.006 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 48 time to evaluate : 0.482 Fit side-chains REVERT: A 38 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.4285 (pp) REVERT: A 54 THR cc_start: 0.8381 (p) cc_final: 0.7984 (m) REVERT: A 60 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7385 (ttmt) REVERT: C 94 PHE cc_start: 0.7930 (p90) cc_final: 0.7709 (p90) REVERT: C 97 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7115 (mttm) REVERT: D 38 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6215 (tp) REVERT: D 54 THR cc_start: 0.8647 (p) cc_final: 0.8435 (p) REVERT: D 83 GLU cc_start: 0.7291 (tt0) cc_final: 0.7032 (mt-10) REVERT: G 38 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6543 (tp) REVERT: J 83 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6881 (tt0) outliers start: 31 outliers final: 19 residues processed: 72 average time/residue: 0.7480 time to fit residues: 57.1004 Evaluate side-chains 67 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4230 Z= 0.457 Angle : 0.938 8.824 5720 Z= 0.547 Chirality : 0.066 0.317 760 Planarity : 0.004 0.014 700 Dihedral : 6.605 18.641 610 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.32 % Favored : 80.68 % Rotamer: Outliers : 9.53 % Allowed : 15.58 % Favored : 74.88 % 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: -4.27 (0.29), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.012 0.003 PHE F 94 TYR 0.018 0.006 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 47 time to evaluate : 0.475 Fit side-chains REVERT: A 54 THR cc_start: 0.8292 (p) cc_final: 0.8050 (m) REVERT: A 60 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7366 (ttmt) REVERT: A 96 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6743 (ttmm) REVERT: B 38 LEU cc_start: 0.4387 (OUTLIER) cc_final: 0.3082 (pp) REVERT: C 54 THR cc_start: 0.8679 (p) cc_final: 0.8422 (m) REVERT: C 80 LYS cc_start: 0.8172 (tttm) cc_final: 0.7925 (tttp) REVERT: C 97 LYS cc_start: 0.7494 (mtpt) cc_final: 0.7165 (mttm) REVERT: D 80 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (tptp) REVERT: D 83 GLU cc_start: 0.7251 (tt0) cc_final: 0.6963 (mt-10) REVERT: J 83 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6828 (tt0) outliers start: 41 outliers final: 25 residues processed: 77 average time/residue: 0.7816 time to fit residues: 63.4639 Evaluate side-chains 74 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 45 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4230 Z= 0.301 Angle : 0.789 7.336 5720 Z= 0.460 Chirality : 0.061 0.280 760 Planarity : 0.003 0.012 700 Dihedral : 6.094 17.735 610 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.63 % Favored : 82.37 % Rotamer: Outliers : 7.91 % Allowed : 17.67 % Favored : 74.42 % 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: -4.12 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.006 HIS C 50 PHE 0.012 0.002 PHE E 94 TYR 0.017 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 45 time to evaluate : 0.485 Fit side-chains REVERT: A 96 LYS cc_start: 0.7058 (ttmt) cc_final: 0.6721 (ttmm) REVERT: B 38 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3353 (pp) REVERT: C 97 LYS cc_start: 0.7354 (mtpt) cc_final: 0.7067 (mttm) REVERT: D 83 GLU cc_start: 0.7214 (tt0) cc_final: 0.6912 (mt-10) REVERT: J 83 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6791 (tt0) outliers start: 34 outliers final: 21 residues processed: 70 average time/residue: 0.7624 time to fit residues: 56.5097 Evaluate side-chains 65 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 42 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 0.0020 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 3.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4230 Z= 0.285 Angle : 0.768 7.124 5720 Z= 0.447 Chirality : 0.060 0.271 760 Planarity : 0.003 0.012 700 Dihedral : 5.907 17.431 610 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 8.14 % Allowed : 18.84 % Favored : 73.02 % 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: -4.01 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.006 HIS D 50 PHE 0.023 0.003 PHE C 94 TYR 0.016 0.004 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 40 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7055 (ttmt) cc_final: 0.6712 (ttmm) REVERT: B 38 LEU cc_start: 0.4031 (OUTLIER) cc_final: 0.3398 (pp) REVERT: C 97 LYS cc_start: 0.7345 (mtpt) cc_final: 0.7059 (mttm) REVERT: D 83 GLU cc_start: 0.7159 (tt0) cc_final: 0.6877 (mt-10) REVERT: I 72 THR cc_start: 0.8058 (p) cc_final: 0.7835 (p) REVERT: J 83 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6822 (tt0) outliers start: 35 outliers final: 26 residues processed: 67 average time/residue: 0.7216 time to fit residues: 51.4902 Evaluate side-chains 68 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 40 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4230 Z= 0.318 Angle : 0.797 7.622 5720 Z= 0.465 Chirality : 0.061 0.285 760 Planarity : 0.003 0.013 700 Dihedral : 5.953 17.198 610 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.64 % Favored : 81.36 % Rotamer: Outliers : 8.60 % Allowed : 19.30 % Favored : 72.09 % 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: -3.99 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.007 HIS F 50 PHE 0.019 0.003 PHE C 94 TYR 0.015 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 41 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6760 (ttmm) REVERT: B 38 LEU cc_start: 0.3921 (OUTLIER) cc_final: 0.3430 (pp) REVERT: C 97 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7182 (mttm) REVERT: D 83 GLU cc_start: 0.7173 (tt0) cc_final: 0.6882 (mt-10) REVERT: I 72 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7947 (p) REVERT: J 83 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6806 (tt0) outliers start: 37 outliers final: 27 residues processed: 68 average time/residue: 0.6334 time to fit residues: 46.0838 Evaluate side-chains 71 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4230 Z= 0.445 Angle : 0.914 8.683 5720 Z= 0.534 Chirality : 0.065 0.313 760 Planarity : 0.003 0.014 700 Dihedral : 6.358 18.238 610 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.34 % Favored : 79.66 % Rotamer: Outliers : 9.53 % Allowed : 17.44 % Favored : 73.02 % 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: -4.06 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS E 50 PHE 0.013 0.003 PHE E 94 TYR 0.017 0.005 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 43 time to evaluate : 0.498 Fit side-chains REVERT: A 96 LYS cc_start: 0.7196 (ttmt) cc_final: 0.6823 (ttmm) REVERT: B 38 LEU cc_start: 0.3708 (OUTLIER) cc_final: 0.2984 (pp) REVERT: C 97 LYS cc_start: 0.7482 (mtpt) cc_final: 0.7149 (mttm) REVERT: D 83 GLU cc_start: 0.7231 (tt0) cc_final: 0.6935 (mt-10) REVERT: I 38 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.4102 (tt) REVERT: I 72 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7856 (p) REVERT: J 83 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6834 (tt0) outliers start: 41 outliers final: 34 residues processed: 72 average time/residue: 0.6529 time to fit residues: 50.0707 Evaluate side-chains 82 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 44 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4230 Z= 0.398 Angle : 0.869 8.321 5720 Z= 0.507 Chirality : 0.064 0.303 760 Planarity : 0.003 0.013 700 Dihedral : 6.284 18.207 610 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.98 % Favored : 81.02 % Rotamer: Outliers : 9.07 % Allowed : 18.60 % Favored : 72.33 % 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: -4.03 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.007 HIS E 50 PHE 0.014 0.003 PHE E 94 TYR 0.016 0.005 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 42 time to evaluate : 0.489 Fit side-chains REVERT: A 96 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6823 (ttmm) REVERT: B 38 LEU cc_start: 0.3731 (OUTLIER) cc_final: 0.2992 (pp) REVERT: C 97 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7153 (mttm) REVERT: D 83 GLU cc_start: 0.7218 (tt0) cc_final: 0.6930 (mt-10) REVERT: G 38 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5181 (tp) REVERT: I 38 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.3980 (tt) REVERT: I 72 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7874 (p) REVERT: J 83 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6841 (tt0) outliers start: 39 outliers final: 33 residues processed: 69 average time/residue: 0.7519 time to fit residues: 55.3148 Evaluate side-chains 80 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 42 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4230 Z= 0.338 Angle : 0.814 7.701 5720 Z= 0.474 Chirality : 0.062 0.290 760 Planarity : 0.003 0.013 700 Dihedral : 6.090 18.060 610 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.15 % Favored : 80.85 % Rotamer: Outliers : 8.84 % Allowed : 18.84 % Favored : 72.33 % 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: -3.97 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.007 HIS E 50 PHE 0.024 0.003 PHE C 94 TYR 0.015 0.004 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 42 time to evaluate : 0.474 Fit side-chains REVERT: A 96 LYS cc_start: 0.7129 (ttmt) cc_final: 0.6761 (ttmm) REVERT: B 38 LEU cc_start: 0.3812 (OUTLIER) cc_final: 0.3257 (pp) REVERT: C 97 LYS cc_start: 0.7564 (mtpt) cc_final: 0.7214 (mttm) REVERT: D 83 GLU cc_start: 0.7197 (tt0) cc_final: 0.6904 (mt-10) REVERT: I 38 LEU cc_start: 0.5448 (OUTLIER) cc_final: 0.4007 (tt) REVERT: I 72 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7858 (p) REVERT: J 83 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6822 (tt0) outliers start: 38 outliers final: 33 residues processed: 67 average time/residue: 0.6529 time to fit residues: 46.7262 Evaluate side-chains 78 residues out of total 430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 41 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.199115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.175622 restraints weight = 4735.461| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.74 r_work: 0.4350 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4256 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4230 Z= 0.403 Angle : 0.874 8.416 5720 Z= 0.511 Chirality : 0.064 0.303 760 Planarity : 0.003 0.013 700 Dihedral : 6.268 18.276 610 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.83 % Favored : 80.17 % Rotamer: Outliers : 8.60 % Allowed : 19.53 % Favored : 71.86 % 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: -3.98 (0.30), residues: 590 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS D 50 PHE 0.014 0.003 PHE E 94 TYR 0.016 0.005 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1530.23 seconds wall clock time: 28 minutes 20.31 seconds (1700.31 seconds total)