Starting phenix.real_space_refine on Fri Aug 22 13:55:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynm_33966/08_2025/7ynm_33966_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynm_33966/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ynm_33966/08_2025/7ynm_33966_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynm_33966/08_2025/7ynm_33966_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ynm_33966/08_2025/7ynm_33966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynm_33966/08_2025/7ynm_33966.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.67, per 1000 atoms: 0.19 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: 0.22 Conformation dependent library (CDL) restraints added in 111.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.09 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: 0.31 Time building geometry restraints manager: 0.30 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: 0.01 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: 3.220 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.230 Find NCS groups from input model: 0.020 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:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- 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= 0.564 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 : 39.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.007 0.002 TYR D 39 PHE 0.011 0.003 PHE B 94 HIS 0.007 0.004 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.01174 ( 3560) covalent geometry : angle 0.99067 ( 4832) hydrogen bonds : bond 0.16545 ( 74) hydrogen bonds : angle 8.98287 ( 222) *********************** 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 : 0.096 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: 0.5608 time to fit residues: 48.3416 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.4844 r_free = 0.4844 target = 0.228042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.203611 restraints weight = 4152.799| |-----------------------------------------------------------------------------| r_work (start): 0.4614 rms_B_bonded: 2.71 r_work: 0.4522 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3560 Z= 0.132 Angle : 0.586 4.280 4832 Z= 0.315 Chirality : 0.053 0.142 608 Planarity : 0.002 0.011 584 Dihedral : 18.915 89.528 520 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 8.43 % Allowed : 8.72 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR D 39 PHE 0.005 0.002 PHE J 94 HIS 0.012 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3560) covalent geometry : angle 0.58624 ( 4832) hydrogen bonds : bond 0.02503 ( 74) hydrogen bonds : angle 6.30516 ( 222) *********************** 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 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 39 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: H 80 LYS cc_start: 0.8048 (tttt) cc_final: 0.7093 (mmpt) outliers start: 29 outliers final: 10 residues processed: 53 average time/residue: 0.5983 time to fit residues: 32.5840 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 : 0.138 ------------------------------------------------------------------------------- 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 C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 overall best weight: 2.3362 ------------------------------------------------------------------------------- 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 = 0.4774 r_free = 0.4774 target = 0.218359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.194569 restraints weight = 4120.248| |-----------------------------------------------------------------------------| r_work (start): 0.4534 rms_B_bonded: 2.51 r_work: 0.4450 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3560 Z= 0.184 Angle : 0.640 4.925 4832 Z= 0.345 Chirality : 0.052 0.141 608 Planarity : 0.003 0.011 584 Dihedral : 19.764 88.043 520 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 8.43 % Allowed : 11.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR J 39 PHE 0.007 0.002 PHE H 94 HIS 0.012 0.005 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 3560) covalent geometry : angle 0.64005 ( 4832) hydrogen bonds : bond 0.02976 ( 74) hydrogen bonds : angle 5.94805 ( 222) *********************** 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 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: H 80 LYS cc_start: 0.8379 (tttt) cc_final: 0.7405 (tptp) outliers start: 29 outliers final: 18 residues processed: 48 average time/residue: 0.5837 time to fit residues: 28.7652 Evaluate side-chains 41 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL 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 D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.207905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.185604 restraints weight = 4293.213| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.53 r_work: 0.4383 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 3560 Z= 0.402 Angle : 0.915 6.369 4832 Z= 0.490 Chirality : 0.058 0.228 608 Planarity : 0.004 0.018 584 Dihedral : 19.999 89.861 520 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 7.56 % Allowed : 14.83 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.36), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR G 39 PHE 0.011 0.003 PHE J 94 HIS 0.016 0.006 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00915 ( 3560) covalent geometry : angle 0.91527 ( 4832) hydrogen bonds : bond 0.03946 ( 74) hydrogen bonds : angle 6.08312 ( 222) *********************** 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: 26 poor density : 24 time to evaluate : 0.166 Fit side-chains REVERT: H 43 LYS cc_start: 0.7901 (mttt) cc_final: 0.6709 (pttp) REVERT: H 80 LYS cc_start: 0.8492 (tttt) cc_final: 0.7577 (tptp) outliers start: 26 outliers final: 21 residues processed: 49 average time/residue: 0.5751 time to fit residues: 28.9733 Evaluate side-chains 42 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 21 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL 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 B residue 57 GLU 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 D residue 55 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 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 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.214511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.191865 restraints weight = 4211.438| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 2.55 r_work: 0.4459 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3560 Z= 0.157 Angle : 0.636 8.305 4832 Z= 0.329 Chirality : 0.051 0.135 608 Planarity : 0.002 0.015 584 Dihedral : 17.823 88.167 520 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.98 % Allowed : 17.73 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 39 PHE 0.007 0.002 PHE J 94 HIS 0.013 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3560) covalent geometry : angle 0.63606 ( 4832) hydrogen bonds : bond 0.02742 ( 74) hydrogen bonds : angle 5.82223 ( 222) *********************** 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 45 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 21 time to evaluate : 0.079 Fit side-chains REVERT: C 45 LYS cc_start: 0.7362 (mtmm) cc_final: 0.6430 (mptt) REVERT: H 80 LYS cc_start: 0.8378 (tttt) cc_final: 0.7355 (tptp) REVERT: I 45 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7029 (mmtt) REVERT: J 83 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7226 (tp30) outliers start: 24 outliers final: 18 residues processed: 42 average time/residue: 0.6239 time to fit residues: 26.9197 Evaluate side-chains 37 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 18 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL 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 B residue 57 GLU 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 D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 0.0040 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 overall best weight: 4.1598 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.208136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.185889 restraints weight = 4265.175| |-----------------------------------------------------------------------------| r_work (start): 0.4488 rms_B_bonded: 2.54 r_work: 0.4399 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3560 Z= 0.281 Angle : 0.795 7.718 4832 Z= 0.412 Chirality : 0.053 0.146 608 Planarity : 0.003 0.014 584 Dihedral : 17.401 82.049 520 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 7.27 % Allowed : 18.90 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR J 39 PHE 0.010 0.003 PHE J 94 HIS 0.015 0.006 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 3560) covalent geometry : angle 0.79457 ( 4832) hydrogen bonds : bond 0.03391 ( 74) hydrogen bonds : angle 5.87024 ( 222) *********************** 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 42 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 17 time to evaluate : 0.114 Fit side-chains REVERT: H 43 LYS cc_start: 0.7840 (mttt) cc_final: 0.6694 (pttp) REVERT: H 80 LYS cc_start: 0.8411 (tttt) cc_final: 0.7309 (tptp) outliers start: 25 outliers final: 19 residues processed: 40 average time/residue: 0.6280 time to fit residues: 25.7908 Evaluate side-chains 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 17 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL 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 B residue 57 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 82 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 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4739 r_free = 0.4739 target = 0.211966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.189550 restraints weight = 4215.608| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.52 r_work: 0.4435 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3560 Z= 0.209 Angle : 0.696 5.838 4832 Z= 0.359 Chirality : 0.052 0.138 608 Planarity : 0.002 0.011 584 Dihedral : 15.541 79.046 520 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.69 % Allowed : 21.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR J 39 PHE 0.009 0.002 PHE J 94 HIS 0.012 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 3560) covalent geometry : angle 0.69593 ( 4832) hydrogen bonds : bond 0.03010 ( 74) hydrogen bonds : angle 5.76680 ( 222) *********************** 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 42 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 19 time to evaluate : 0.170 Fit side-chains REVERT: H 80 LYS cc_start: 0.8248 (tttt) cc_final: 0.7341 (tptp) REVERT: I 45 LYS cc_start: 0.7828 (mtmt) cc_final: 0.6980 (mmtt) REVERT: J 83 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7234 (tp30) outliers start: 23 outliers final: 19 residues processed: 40 average time/residue: 0.5897 time to fit residues: 24.3356 Evaluate side-chains 37 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 17 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL 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 B residue 57 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.4748 r_free = 0.4748 target = 0.211377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.189213 restraints weight = 4277.403| |-----------------------------------------------------------------------------| r_work (start): 0.4541 rms_B_bonded: 2.49 r_work: 0.4449 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3560 Z= 0.193 Angle : 0.673 5.589 4832 Z= 0.349 Chirality : 0.051 0.136 608 Planarity : 0.002 0.011 584 Dihedral : 14.078 80.706 520 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.10 % Allowed : 22.67 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 39 PHE 0.009 0.002 PHE J 94 HIS 0.012 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3560) covalent geometry : angle 0.67263 ( 4832) hydrogen bonds : bond 0.02969 ( 74) hydrogen bonds : angle 5.76952 ( 222) *********************** 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 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 17 time to evaluate : 0.082 Fit side-chains REVERT: C 45 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6464 (mptt) REVERT: H 80 LYS cc_start: 0.8203 (tttt) cc_final: 0.7303 (mmpt) REVERT: I 45 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7020 (mmtt) REVERT: J 83 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7233 (tp30) outliers start: 21 outliers final: 19 residues processed: 37 average time/residue: 0.6124 time to fit residues: 23.3165 Evaluate side-chains 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 16 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 VAL 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 B residue 57 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4796 r_free = 0.4796 target = 0.216336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.193842 restraints weight = 4176.846| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.52 r_work: 0.4490 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3560 Z= 0.130 Angle : 0.593 5.505 4832 Z= 0.306 Chirality : 0.050 0.132 608 Planarity : 0.002 0.012 584 Dihedral : 12.694 81.873 520 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.81 % Allowed : 22.97 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 TYR 0.006 0.001 TYR J 39 PHE 0.008 0.002 PHE J 94 HIS 0.012 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3560) covalent geometry : angle 0.59269 ( 4832) hydrogen bonds : bond 0.02479 ( 74) hydrogen bonds : angle 5.67780 ( 222) *********************** 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 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 16 time to evaluate : 0.141 Fit side-chains REVERT: C 45 LYS cc_start: 0.7350 (mtmm) cc_final: 0.6479 (mptt) REVERT: G 61 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7814 (mm-30) REVERT: H 80 LYS cc_start: 0.8113 (tttt) cc_final: 0.7220 (tptp) REVERT: I 45 LYS cc_start: 0.7813 (mtmt) cc_final: 0.7017 (mmtt) REVERT: J 83 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7102 (tp30) outliers start: 20 outliers final: 17 residues processed: 35 average time/residue: 0.6197 time to fit residues: 22.4174 Evaluate side-chains 34 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 16 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL 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 D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.4724 r_free = 0.4724 target = 0.210336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.187817 restraints weight = 4283.808| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 2.56 r_work: 0.4419 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3560 Z= 0.249 Angle : 0.737 5.730 4832 Z= 0.388 Chirality : 0.052 0.142 608 Planarity : 0.003 0.013 584 Dihedral : 13.342 83.898 520 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 5.52 % Allowed : 23.84 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.27 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR J 39 PHE 0.009 0.002 PHE J 94 HIS 0.012 0.005 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 3560) covalent geometry : angle 0.73698 ( 4832) hydrogen bonds : bond 0.03297 ( 74) hydrogen bonds : angle 5.81837 ( 222) ********************** 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 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 17 time to evaluate : 0.130 Fit side-chains REVERT: H 43 LYS cc_start: 0.7821 (mttt) cc_final: 0.6658 (pttp) REVERT: H 80 LYS cc_start: 0.8300 (tttt) cc_final: 0.7367 (mmpt) outliers start: 19 outliers final: 17 residues processed: 35 average time/residue: 0.5998 time to fit residues: 21.7067 Evaluate side-chains 33 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL 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 D residue 44 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 55 VAL 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 I residue 57 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.0000 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.4839 r_free = 0.4839 target = 0.220473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.198079 restraints weight = 4149.685| |-----------------------------------------------------------------------------| r_work (start): 0.4626 rms_B_bonded: 2.50 r_work: 0.4536 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3560 Z= 0.097 Angle : 0.541 5.518 4832 Z= 0.281 Chirality : 0.051 0.126 608 Planarity : 0.002 0.011 584 Dihedral : 11.436 84.804 520 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.36 % Allowed : 25.00 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.007 0.002 PHE J 94 HIS 0.012 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 3560) covalent geometry : angle 0.54134 ( 4832) hydrogen bonds : bond 0.02238 ( 74) hydrogen bonds : angle 5.74207 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1155.54 seconds wall clock time: 20 minutes 32.33 seconds (1232.33 seconds total)