Starting phenix.real_space_refine on Wed Mar 5 21:12:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynm_33966/03_2025/7ynm_33966_neut.cif" } resolution = 2.9 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= 0.003 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 8 5.16 5 C 2256 2.51 5 N 600 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3528 Number of models: 1 Model: "" Number of chains: 3 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: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, G, H, D, I, J Time building chain proxies: 2.22, per 1000 atoms: 0.63 Number of scatterers: 3528 At special positions: 0 Unit cell: (95.45, 105.41, 34.86, 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 8 16.00 O 664 8.00 N 600 7.00 C 2256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 444.8 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 832 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 65.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 66 removed outlier: 6.909A pdb=" N GLU C 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY A 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA C 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU A 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS C 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 59 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU G 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY C 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA C 53 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR G 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 55 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA G 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU C 57 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS G 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 59 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU I 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY G 47 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL I 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA G 53 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR I 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL G 55 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA I 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU G 57 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS I 58 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR G 59 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.947A pdb=" N VAL C 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 71 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR C 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY A 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA C 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN A 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS C 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL G 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 71 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR G 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY C 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA G 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN C 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS G 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL G 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL I 70 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL G 71 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR I 72 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY G 73 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL G 77 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA I 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN G 79 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS I 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR G 81 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL I 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 92 removed outlier: 8.903A pdb=" N GLY A 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA C 89 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA C 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA A 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLY C 86 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N ALA G 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE C 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA G 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLY G 86 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA I 89 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE G 88 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA I 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA G 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 45 through 66 removed outlier: 6.909A pdb=" N GLU D 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY B 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL D 52 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA B 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR D 54 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL B 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA D 56 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS D 58 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 59 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLU B 46 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N VAL J 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N GLY J 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N HIS B 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ALA J 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N VAL B 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 10.356A pdb=" N VAL J 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N THR B 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N GLU J 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N ALA B 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N THR J 59 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 58 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N GLU J 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS B 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL J 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ASN J 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR B 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU J 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL J 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA H 53 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR J 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL H 55 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA J 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU H 57 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS J 58 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR H 59 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.948A pdb=" N VAL D 70 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR D 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY B 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA D 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN B 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS D 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL B 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N GLY J 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N THR B 72 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N THR J 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL B 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL J 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA B 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N GLN J 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA B 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N THR J 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N LYS B 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL J 70 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL H 71 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR J 72 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY H 73 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL H 77 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA J 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN H 79 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS J 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR H 81 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL J 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 86 through 92 removed outlier: 8.903A pdb=" N GLY B 86 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA D 89 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE B 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA D 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER B 87 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE J 88 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N GLY H 86 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N ALA J 89 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE H 88 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA J 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA H 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 0.77 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.31: 576 1.31 - 1.40: 728 1.40 - 1.49: 701 1.49 - 1.58: 1539 1.58 - 1.67: 16 Bond restraints: 3560 Sorted by residual: bond pdb=" C5 TFX B 202 " pdb=" C8 TFX B 202 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C5 TFX G 202 " pdb=" C8 TFX G 202 " ideal model delta sigma weight residual 1.435 1.559 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C5 TFX H 202 " pdb=" C8 TFX H 202 " ideal model delta sigma weight residual 1.435 1.558 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C5 TFX A 202 " pdb=" C8 TFX A 202 " ideal model delta sigma weight residual 1.435 1.558 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C2 TFX A 201 " pdb=" N2 TFX A 201 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 3555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 4672 2.14 - 4.28: 100 4.28 - 6.42: 40 6.42 - 8.56: 12 8.56 - 10.70: 8 Bond angle restraints: 4832 Sorted by residual: angle pdb=" C5 TFX H 202 " pdb=" C8 TFX H 202 " pdb=" S1 TFX H 202 " ideal model delta sigma weight residual 120.55 131.25 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C5 TFX B 202 " pdb=" C8 TFX B 202 " pdb=" S1 TFX B 202 " ideal model delta sigma weight residual 120.55 131.24 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C5 TFX A 202 " pdb=" C8 TFX A 202 " pdb=" S1 TFX A 202 " ideal model delta sigma weight residual 120.55 131.22 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C5 TFX G 202 " pdb=" C8 TFX G 202 " pdb=" S1 TFX G 202 " ideal model delta sigma weight residual 120.55 131.18 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" C10 TFX B 202 " pdb=" S1 TFX B 202 " pdb=" C8 TFX B 202 " ideal model delta sigma weight residual 91.28 100.91 -9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 4827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1896 16.52 - 33.04: 64 33.04 - 49.55: 16 49.55 - 66.07: 16 66.07 - 82.59: 16 Dihedral angle restraints: 2008 sinusoidal: 688 harmonic: 1320 Sorted by residual: dihedral pdb=" CA GLY I 93 " pdb=" C GLY I 93 " pdb=" N PHE I 94 " pdb=" CA PHE I 94 " ideal model delta harmonic sigma weight residual 180.00 167.21 12.79 0 5.00e+00 4.00e-02 6.54e+00 dihedral pdb=" CA GLY J 93 " pdb=" C GLY J 93 " pdb=" N PHE J 94 " pdb=" CA PHE J 94 " ideal model delta harmonic sigma weight residual 180.00 167.23 12.77 0 5.00e+00 4.00e-02 6.52e+00 dihedral pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" N PHE C 94 " pdb=" CA PHE C 94 " ideal model delta harmonic sigma weight residual 180.00 167.23 12.77 0 5.00e+00 4.00e-02 6.52e+00 ... (remaining 2005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 199 0.025 - 0.051: 223 0.051 - 0.076: 63 0.076 - 0.101: 75 0.101 - 0.127: 48 Chirality restraints: 608 Sorted by residual: chirality pdb=" CA VAL J 49 " pdb=" N VAL J 49 " pdb=" C VAL J 49 " pdb=" CB VAL J 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 605 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 TFX H 202 " -0.028 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" C3 TFX H 202 " -0.030 2.00e-02 2.50e+03 pdb=" C4 TFX H 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX H 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX H 202 " -0.009 2.00e-02 2.50e+03 pdb=" C7 TFX H 202 " -0.025 2.00e-02 2.50e+03 pdb=" C8 TFX H 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX H 202 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TFX G 202 " -0.029 2.00e-02 2.50e+03 3.08e-02 1.90e+01 pdb=" C3 TFX G 202 " -0.029 2.00e-02 2.50e+03 pdb=" C4 TFX G 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX G 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX G 202 " -0.008 2.00e-02 2.50e+03 pdb=" C7 TFX G 202 " -0.024 2.00e-02 2.50e+03 pdb=" C8 TFX G 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX G 202 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 TFX A 202 " -0.028 2.00e-02 2.50e+03 3.07e-02 1.89e+01 pdb=" C3 TFX A 202 " -0.029 2.00e-02 2.50e+03 pdb=" C4 TFX A 202 " -0.007 2.00e-02 2.50e+03 pdb=" C5 TFX A 202 " -0.001 2.00e-02 2.50e+03 pdb=" C6 TFX A 202 " -0.009 2.00e-02 2.50e+03 pdb=" C7 TFX A 202 " -0.024 2.00e-02 2.50e+03 pdb=" C8 TFX A 202 " 0.037 2.00e-02 2.50e+03 pdb=" N2 TFX A 202 " 0.062 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 303 2.76 - 3.29: 3286 3.29 - 3.83: 5736 3.83 - 4.36: 6333 4.36 - 4.90: 13181 Nonbonded interactions: 28839 Sorted by model distance: nonbonded pdb=" CE LYS B 80 " pdb=" C16 TFX B 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS H 80 " pdb=" C16 TFX H 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS A 80 " pdb=" C16 TFX A 201 " model vdw 2.219 3.860 nonbonded pdb=" CE LYS G 80 " pdb=" C16 TFX G 201 " model vdw 2.220 3.860 nonbonded pdb=" CE LYS C 80 " pdb=" C16 TFX G 202 " model vdw 2.255 3.860 ... (remaining 28834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.012 0.124 3560 Z= 0.719 Angle : 0.991 10.697 4832 Z= 0.415 Chirality : 0.055 0.127 608 Planarity : 0.004 0.031 584 Dihedral : 14.588 82.585 1176 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 39.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.80 (0.34), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.011 0.003 PHE B 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.357 Fit side-chains REVERT: H 46 GLU cc_start: 0.5731 (mt-10) cc_final: 0.5422 (tt0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 1.1885 time to fit residues: 102.6291 Evaluate side-chains 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.234074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.208910 restraints weight = 4018.931| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 2.76 r_work: 0.4575 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3560 Z= 0.149 Angle : 0.559 4.158 4832 Z= 0.298 Chirality : 0.052 0.138 608 Planarity : 0.002 0.011 584 Dihedral : 18.575 89.974 520 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.10 % Allowed : 11.63 % Favored : 82.27 % 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: -2.25 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.004 HIS C 50 PHE 0.005 0.001 PHE G 94 TYR 0.008 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7367 (mm-30) REVERT: C 62 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: J 61 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7283 (mt-10) outliers start: 21 outliers final: 8 residues processed: 48 average time/residue: 1.3456 time to fit residues: 66.5034 Evaluate side-chains 37 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.0570 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.230066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.205708 restraints weight = 4059.429| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 2.61 r_work: 0.4566 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3560 Z= 0.168 Angle : 0.524 4.344 4832 Z= 0.289 Chirality : 0.051 0.135 608 Planarity : 0.002 0.011 584 Dihedral : 18.282 88.597 520 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.52 % Allowed : 15.12 % Favored : 79.36 % 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: -1.94 (0.40), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.006 HIS I 50 PHE 0.006 0.002 PHE C 94 TYR 0.005 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.342 Fit side-chains REVERT: C 62 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: I 45 LYS cc_start: 0.7771 (mtmt) cc_final: 0.6658 (mmmt) outliers start: 19 outliers final: 9 residues processed: 43 average time/residue: 1.3437 time to fit residues: 59.5123 Evaluate side-chains 32 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.228389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.204196 restraints weight = 4040.317| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 2.56 r_work: 0.4566 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3560 Z= 0.164 Angle : 0.505 4.094 4832 Z= 0.278 Chirality : 0.051 0.134 608 Planarity : 0.002 0.010 584 Dihedral : 16.144 89.624 520 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.40 % Allowed : 14.83 % Favored : 78.78 % 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: -1.84 (0.40), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS H 50 PHE 0.006 0.002 PHE C 94 TYR 0.006 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 28 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 45 LYS cc_start: 0.7791 (mtmt) cc_final: 0.6756 (mmmt) REVERT: J 45 LYS cc_start: 0.7498 (mtmm) cc_final: 0.7205 (mtmm) outliers start: 22 outliers final: 12 residues processed: 48 average time/residue: 1.5482 time to fit residues: 76.1589 Evaluate side-chains 34 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS C 62 GLN H 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.219926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.197563 restraints weight = 4108.523| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.39 r_work: 0.4516 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3560 Z= 0.276 Angle : 0.600 4.501 4832 Z= 0.330 Chirality : 0.052 0.141 608 Planarity : 0.002 0.011 584 Dihedral : 16.228 89.558 520 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.52 % Allowed : 17.44 % Favored : 77.03 % 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: -2.01 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS H 50 PHE 0.008 0.002 PHE C 94 TYR 0.008 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: I 45 LYS cc_start: 0.7795 (mtmt) cc_final: 0.6931 (mmmt) REVERT: J 45 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7460 (mtmm) outliers start: 19 outliers final: 14 residues processed: 43 average time/residue: 1.5552 time to fit residues: 68.6465 Evaluate side-chains 37 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.219045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.196831 restraints weight = 4147.807| |-----------------------------------------------------------------------------| r_work (start): 0.4605 rms_B_bonded: 2.39 r_work: 0.4519 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3560 Z= 0.253 Angle : 0.575 4.818 4832 Z= 0.317 Chirality : 0.052 0.144 608 Planarity : 0.002 0.012 584 Dihedral : 15.393 88.920 520 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.10 % Allowed : 18.31 % Favored : 75.58 % 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: -2.08 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS H 50 PHE 0.007 0.002 PHE C 94 TYR 0.006 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 24 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7608 (ptpp) cc_final: 0.7404 (pttt) REVERT: H 57 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6415 (pt0) REVERT: I 45 LYS cc_start: 0.7865 (mtmt) cc_final: 0.6971 (mmmt) outliers start: 21 outliers final: 14 residues processed: 41 average time/residue: 1.4478 time to fit residues: 61.0167 Evaluate side-chains 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 21 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.216608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.194362 restraints weight = 4135.643| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 2.42 r_work: 0.4510 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3560 Z= 0.264 Angle : 0.594 4.731 4832 Z= 0.325 Chirality : 0.052 0.148 608 Planarity : 0.002 0.017 584 Dihedral : 15.106 85.066 520 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.81 % Allowed : 19.77 % 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: -2.11 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.006 HIS G 50 PHE 0.008 0.002 PHE C 94 TYR 0.007 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7666 (ptpp) cc_final: 0.7378 (pttt) REVERT: H 57 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6474 (pt0) REVERT: I 45 LYS cc_start: 0.7872 (mtmt) cc_final: 0.6972 (mmmt) outliers start: 20 outliers final: 15 residues processed: 41 average time/residue: 1.4828 time to fit residues: 62.4411 Evaluate side-chains 35 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.213102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.191209 restraints weight = 4103.098| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.41 r_work: 0.4479 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3560 Z= 0.366 Angle : 0.692 6.360 4832 Z= 0.374 Chirality : 0.053 0.147 608 Planarity : 0.003 0.012 584 Dihedral : 16.085 79.160 520 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 6.40 % Allowed : 19.19 % 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: -2.32 (0.36), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.006 HIS H 50 PHE 0.008 0.002 PHE D 94 TYR 0.008 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 21 time to evaluate : 0.357 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 38 average time/residue: 1.3940 time to fit residues: 54.5637 Evaluate side-chains 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 20 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.220259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.198076 restraints weight = 4026.724| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 2.38 r_work: 0.4558 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3560 Z= 0.177 Angle : 0.541 5.447 4832 Z= 0.292 Chirality : 0.051 0.131 608 Planarity : 0.002 0.016 584 Dihedral : 13.854 76.008 520 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.52 % Allowed : 20.35 % Favored : 74.13 % 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: -2.05 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.004 HIS H 50 PHE 0.007 0.002 PHE J 94 TYR 0.005 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 25 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7594 (pttm) REVERT: D 58 LYS cc_start: 0.6879 (mttt) cc_final: 0.5841 (pmtt) REVERT: I 45 LYS cc_start: 0.7817 (mtmt) cc_final: 0.6873 (mmmt) outliers start: 19 outliers final: 13 residues processed: 41 average time/residue: 1.3533 time to fit residues: 57.1499 Evaluate side-chains 34 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 40 optimal weight: 0.2980 chunk 18 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS I 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.222018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.199956 restraints weight = 4085.121| |-----------------------------------------------------------------------------| r_work (start): 0.4673 rms_B_bonded: 2.37 r_work: 0.4585 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3560 Z= 0.165 Angle : 0.530 5.345 4832 Z= 0.287 Chirality : 0.051 0.132 608 Planarity : 0.002 0.016 584 Dihedral : 11.961 79.765 520 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.07 % Allowed : 22.97 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.005 HIS H 50 PHE 0.007 0.002 PHE J 94 TYR 0.004 0.001 TYR J 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.6290 (mtmm) cc_final: 0.6025 (mtpt) REVERT: C 45 LYS cc_start: 0.7901 (ptpt) cc_final: 0.7612 (pttm) REVERT: D 58 LYS cc_start: 0.6685 (mttt) cc_final: 0.5731 (pmtt) REVERT: I 45 LYS cc_start: 0.7842 (mtmt) cc_final: 0.6984 (mmmt) outliers start: 14 outliers final: 12 residues processed: 35 average time/residue: 1.5054 time to fit residues: 54.2060 Evaluate side-chains 33 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.216939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.195045 restraints weight = 4084.410| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 2.38 r_work: 0.4521 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3560 Z= 0.274 Angle : 0.624 5.994 4832 Z= 0.342 Chirality : 0.052 0.142 608 Planarity : 0.002 0.015 584 Dihedral : 12.825 77.375 520 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.65 % Allowed : 22.09 % Favored : 73.26 % 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: -2.06 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS C 50 PHE 0.007 0.002 PHE J 94 TYR 0.007 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2400.42 seconds wall clock time: 41 minutes 55.67 seconds (2515.67 seconds total)