Starting phenix.real_space_refine on Tue Feb 11 02:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynm_33966/02_2025/7ynm_33966_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynm_33966/02_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_33966/02_2025/7ynm_33966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynm_33966/02_2025/7ynm_33966.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynm_33966/02_2025/7ynm_33966_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynm_33966/02_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-5592/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: 2.45, per 1000 atoms: 0.69 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: 0.84 Conformation dependent library (CDL) restraints added in 433.6 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: 0.36 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: 0.76 Time building geometry restraints manager: 0.95 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 12.330 Find NCS groups from input model: 0.080 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- 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 : 0.428 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: 1.2653 time to fit residues: 109.2079 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 : 0.377 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4884 r_free = 0.4884 target = 0.232008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.206994 restraints weight = 4032.181| |-----------------------------------------------------------------------------| r_work (start): 0.4647 rms_B_bonded: 2.74 r_work: 0.4557 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3560 Z= 0.157 Angle : 0.574 4.191 4832 Z= 0.305 Chirality : 0.052 0.138 608 Planarity : 0.002 0.011 584 Dihedral : 18.674 89.681 520 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 6.98 % Allowed : 10.76 % 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: -2.23 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS C 50 PHE 0.005 0.001 PHE J 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 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7297 (mm-30) REVERT: H 80 LYS cc_start: 0.7920 (tttt) cc_final: 0.6768 (mmpt) outliers start: 24 outliers final: 9 residues processed: 50 average time/residue: 1.2932 time to fit residues: 66.7643 Evaluate side-chains 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 D residue 44 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 7.9990 chunk 37 optimal weight: 0.0670 chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.6122 ------------------------------------------------------------------------------- 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 = 0.4764 r_free = 0.4764 target = 0.217100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.193591 restraints weight = 4071.249| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 2.48 r_work: 0.4442 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3560 Z= 0.321 Angle : 0.662 5.547 4832 Z= 0.359 Chirality : 0.052 0.142 608 Planarity : 0.003 0.012 584 Dihedral : 19.729 86.995 520 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 7.85 % Allowed : 12.50 % Favored : 79.65 % 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: -2.20 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.007 HIS I 50 PHE 0.008 0.002 PHE H 94 TYR 0.009 0.002 TYR J 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 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 28 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: H 80 LYS cc_start: 0.8400 (tttt) cc_final: 0.7631 (tptp) outliers start: 27 outliers final: 16 residues processed: 48 average time/residue: 1.5562 time to fit residues: 76.6527 Evaluate side-chains 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 55 VAL Chi-restraints excluded: chain I residue 57 GLU 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: 1.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.217870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.195310 restraints weight = 4093.450| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.44 r_work: 0.4495 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4970 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= 0.245 Angle : 0.591 4.448 4832 Z= 0.318 Chirality : 0.051 0.135 608 Planarity : 0.002 0.012 584 Dihedral : 18.593 89.431 520 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.10 % Allowed : 15.99 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS H 50 PHE 0.007 0.002 PHE B 94 TYR 0.007 0.002 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 47 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: H 80 LYS cc_start: 0.8278 (tttt) cc_final: 0.7440 (tptp) REVERT: I 45 LYS cc_start: 0.7773 (mtmt) cc_final: 0.6929 (mmmt) outliers start: 21 outliers final: 16 residues processed: 45 average time/residue: 1.4853 time to fit residues: 68.6413 Evaluate side-chains 37 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 21 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.0870 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- 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 = 0.4791 r_free = 0.4791 target = 0.216493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.193518 restraints weight = 4176.501| |-----------------------------------------------------------------------------| r_work (start): 0.4567 rms_B_bonded: 2.53 r_work: 0.4482 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3560 Z= 0.239 Angle : 0.587 5.058 4832 Z= 0.314 Chirality : 0.051 0.142 608 Planarity : 0.002 0.011 584 Dihedral : 17.198 83.046 520 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 6.10 % Allowed : 17.44 % Favored : 76.45 % 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: -2.03 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (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 G 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 43 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 22 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.7185 (mtmm) cc_final: 0.6324 (mptt) REVERT: H 80 LYS cc_start: 0.8319 (tttt) cc_final: 0.7473 (tptp) REVERT: I 45 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7026 (mmmt) outliers start: 21 outliers final: 16 residues processed: 40 average time/residue: 1.4442 time to fit residues: 59.5332 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 : 0.384 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 21 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 = 0.4774 r_free = 0.4774 target = 0.214788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.192004 restraints weight = 4266.418| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 2.53 r_work: 0.4463 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5508 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= 0.262 Angle : 0.610 5.102 4832 Z= 0.323 Chirality : 0.051 0.142 608 Planarity : 0.002 0.015 584 Dihedral : 16.225 82.428 520 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.40 % Allowed : 17.44 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (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 0.012 0.005 HIS H 50 PHE 0.007 0.002 PHE J 94 TYR 0.006 0.001 TYR G 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 43 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 21 time to evaluate : 0.405 Fit side-chains REVERT: C 45 LYS cc_start: 0.7283 (mtmm) cc_final: 0.6422 (mptt) REVERT: I 45 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7035 (mmmt) outliers start: 22 outliers final: 17 residues processed: 41 average time/residue: 1.4658 time to fit residues: 61.9010 Evaluate side-chains 34 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 17 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 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 = 0.4749 r_free = 0.4749 target = 0.212682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.190790 restraints weight = 4145.669| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.42 r_work: 0.4454 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5711 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= 0.333 Angle : 0.679 6.029 4832 Z= 0.359 Chirality : 0.052 0.137 608 Planarity : 0.003 0.018 584 Dihedral : 16.098 87.557 520 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 6.10 % Allowed : 19.19 % Favored : 74.71 % 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: -2.20 (0.37), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.006 HIS I 50 PHE 0.008 0.002 PHE J 94 TYR 0.007 0.002 TYR J 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 43 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 22 time to evaluate : 0.348 Fit side-chains REVERT: C 45 LYS cc_start: 0.7429 (mtmm) cc_final: 0.6528 (mptt) REVERT: H 43 LYS cc_start: 0.7828 (mttt) cc_final: 0.6674 (pttp) REVERT: I 45 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7128 (mmtt) outliers start: 21 outliers final: 17 residues processed: 41 average time/residue: 1.5192 time to fit residues: 64.0495 Evaluate side-chains 36 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.216900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.194603 restraints weight = 4160.197| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.47 r_work: 0.4507 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3560 Z= 0.201 Angle : 0.577 5.568 4832 Z= 0.301 Chirality : 0.051 0.132 608 Planarity : 0.002 0.010 584 Dihedral : 14.410 82.428 520 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.23 % Allowed : 20.35 % 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: -2.07 (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 0.012 0.005 HIS H 50 PHE 0.007 0.002 PHE J 94 TYR 0.006 0.001 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 42 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.345 Fit side-chains REVERT: C 45 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6395 (mptt) REVERT: D 58 LYS cc_start: 0.6912 (mttt) cc_final: 0.6073 (pmtt) REVERT: I 45 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7058 (mmmt) outliers start: 18 outliers final: 17 residues processed: 41 average time/residue: 1.4102 time to fit residues: 59.5797 Evaluate side-chains 35 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 0.0980 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.212510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.190223 restraints weight = 4150.162| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.48 r_work: 0.4451 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3560 Z= 0.335 Angle : 0.683 5.340 4832 Z= 0.361 Chirality : 0.052 0.135 608 Planarity : 0.003 0.019 584 Dihedral : 15.312 89.660 520 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 5.52 % Allowed : 21.22 % 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: -2.16 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.008 HIS C 50 PHE 0.008 0.002 PHE J 94 TYR 0.008 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 38 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 19 time to evaluate : 0.384 Fit side-chains REVERT: C 45 LYS cc_start: 0.7406 (mtmm) cc_final: 0.6507 (mptt) REVERT: H 43 LYS cc_start: 0.7786 (mttt) cc_final: 0.6629 (pttp) REVERT: I 45 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7114 (mmmt) outliers start: 19 outliers final: 17 residues processed: 37 average time/residue: 1.3979 time to fit residues: 53.3741 Evaluate side-chains 35 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.219567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.197232 restraints weight = 4078.112| |-----------------------------------------------------------------------------| r_work (start): 0.4625 rms_B_bonded: 2.41 r_work: 0.4531 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3560 Z= 0.171 Angle : 0.543 4.739 4832 Z= 0.290 Chirality : 0.051 0.132 608 Planarity : 0.002 0.015 584 Dihedral : 14.646 89.393 520 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.23 % Allowed : 21.51 % 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: -2.02 (0.39), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.006 HIS C 50 PHE 0.007 0.002 PHE J 94 TYR 0.006 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 42 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 24 time to evaluate : 0.375 Fit side-chains REVERT: C 45 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6384 (mptt) REVERT: D 58 LYS cc_start: 0.6762 (mttt) cc_final: 0.5914 (pmtt) REVERT: H 80 LYS cc_start: 0.8197 (tttt) cc_final: 0.7257 (mmpt) REVERT: I 45 LYS cc_start: 0.7860 (mtmt) cc_final: 0.7041 (mmmt) outliers start: 18 outliers final: 16 residues processed: 41 average time/residue: 1.5252 time to fit residues: 64.2424 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 : 0.377 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** G 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.216455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.194013 restraints weight = 4140.332| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.41 r_work: 0.4503 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3560 Z= 0.249 Angle : 0.599 4.901 4832 Z= 0.320 Chirality : 0.051 0.133 608 Planarity : 0.002 0.016 584 Dihedral : 14.846 88.025 520 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.94 % Allowed : 21.80 % 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: -2.02 (0.38), residues: 472 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.006 HIS G 50 PHE 0.007 0.002 PHE J 94 TYR 0.006 0.001 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.01 seconds wall clock time: 43 minutes 22.94 seconds (2602.94 seconds total)