Starting phenix.real_space_refine on Tue Mar 3 17:48:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2026/6sdz_10150.map" } resolution = 2.97 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= 0.001 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 22 5.16 5 C 5115 2.51 5 N 1298 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7909 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.26 Number of scatterers: 7909 At special positions: 0 Unit cell: (82.16, 75.92, 68.64, 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 22 16.00 O 1474 8.00 N 1298 7.00 C 5115 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: 0.92 Conformation dependent library (CDL) restraints added in 312.4 milliseconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 6.222A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL I 14 " --> pdb=" O LYS J 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.125A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL E 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL F 20 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL G 20 " --> pdb=" O ARG H 21 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL H 20 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL I 20 " --> pdb=" O ARG J 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.308A pdb=" N ILE A 26 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA B 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A 28 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS B 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A 30 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE B 33 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 32 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA D 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 28 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HIS D 31 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET C 30 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE D 33 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 32 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE D 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ALA E 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 28 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS E 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET D 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE E 33 " --> pdb=" O MET D 30 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE F 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA G 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL F 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N HIS G 31 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 30 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE G 33 " --> pdb=" O MET F 30 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL F 32 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE H 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA I 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL H 28 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS I 31 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET H 30 " --> pdb=" O HIS I 31 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE I 33 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL H 32 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE I 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA J 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL I 28 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N HIS J 31 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET I 30 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE J 33 " --> pdb=" O MET I 30 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL I 32 " --> pdb=" O PHE J 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.306A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR G 59 " --> pdb=" O THR H 60 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU H 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU G 61 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR H 59 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU I 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU H 61 " --> pdb=" O GLU I 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR I 59 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU J 62 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLU I 61 " --> pdb=" O GLU J 62 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR J 59 " --> pdb=" O THR K 60 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLU K 62 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU J 61 " --> pdb=" O GLU K 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.438A pdb=" N GLU H 72 " --> pdb=" O ILE I 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 9.165A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS B 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N TRP C 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR B 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N LYS C 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.674A pdb=" N TRP D 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR C 78 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N LYS E 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N TRP F 79 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR E 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LYS F 76 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N TRP G 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR F 78 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N LYS G 76 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N TRP H 79 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR G 78 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS H 76 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 9.652A pdb=" N TRP I 79 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N TYR H 78 " --> pdb=" O TRP I 79 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS I 76 " --> pdb=" O SER J 77 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N TRP J 79 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 78 " --> pdb=" O TRP J 79 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N LYS J 76 " --> pdb=" O SER K 77 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N TRP K 79 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR J 78 " --> pdb=" O TRP K 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.877A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR G 114 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR H 114 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR I 114 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR J 114 " --> pdb=" O SER K 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.589A pdb=" N THR E 119 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL F 122 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 83 through 84 removed outlier: 3.501A pdb=" N ILE E 84 " --> pdb=" O GLY F 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 192 hydrogen bonds defined for protein. 576 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1351 1.32 - 1.44: 2140 1.44 - 1.57: 4559 1.57 - 1.69: 2 1.69 - 1.81: 44 Bond restraints: 8096 Sorted by residual: bond pdb=" CE1 HIS A 31 " pdb=" NE2 HIS A 31 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER D 112 " pdb=" CB SER D 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" CA SER G 112 " pdb=" CB SER G 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.62e+00 bond pdb=" CA SER H 112 " pdb=" CB SER H 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.47e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10111 1.95 - 3.91: 825 3.91 - 5.86: 59 5.86 - 7.82: 3 7.82 - 9.77: 2 Bond angle restraints: 11000 Sorted by residual: angle pdb=" CD1 LEU G 58 " pdb=" CG LEU G 58 " pdb=" CD2 LEU G 58 " ideal model delta sigma weight residual 110.80 101.03 9.77 2.20e+00 2.07e-01 1.97e+01 angle pdb=" CD1 LEU I 58 " pdb=" CG LEU I 58 " pdb=" CD2 LEU I 58 " ideal model delta sigma weight residual 110.80 102.17 8.63 2.20e+00 2.07e-01 1.54e+01 angle pdb=" O ILE C 68 " pdb=" C ILE C 68 " pdb=" N TYR C 69 " ideal model delta sigma weight residual 121.83 125.46 -3.63 1.03e+00 9.43e-01 1.24e+01 angle pdb=" CA GLU G 62 " pdb=" C GLU G 62 " pdb=" O GLU G 62 " ideal model delta sigma weight residual 121.40 117.46 3.94 1.13e+00 7.83e-01 1.22e+01 angle pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " pdb=" CD GLU H 61 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+01 ... (remaining 10995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.00: 4047 11.00 - 21.99: 486 21.99 - 32.99: 172 32.99 - 43.98: 70 43.98 - 54.98: 10 Dihedral angle restraints: 4785 sinusoidal: 1826 harmonic: 2959 Sorted by residual: dihedral pdb=" C GLU E 63 " pdb=" N GLU E 63 " pdb=" CA GLU E 63 " pdb=" CB GLU E 63 " ideal model delta harmonic sigma weight residual -122.60 -131.36 8.76 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" CA ILE K 26 " pdb=" C ILE K 26 " pdb=" N ASN K 27 " pdb=" CA ASN K 27 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N ASN H 27 " pdb=" CA ASN H 27 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 846 0.076 - 0.151: 364 0.151 - 0.227: 52 0.227 - 0.303: 20 0.303 - 0.379: 5 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CG LEU G 58 " pdb=" CB LEU G 58 " pdb=" CD1 LEU G 58 " pdb=" CD2 LEU G 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB VAL K 16 " pdb=" CA VAL K 16 " pdb=" CG1 VAL K 16 " pdb=" CG2 VAL K 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 1284 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 64 " 0.013 2.00e-02 2.50e+03 4.88e-02 4.16e+01 pdb=" CG PHE K 64 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE K 64 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE K 64 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE K 64 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE K 64 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE K 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.022 2.00e-02 2.50e+03 4.16e-02 3.47e+01 pdb=" CG TYR A 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 114 " -0.019 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR J 114 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR J 114 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR J 114 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR J 114 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 114 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR J 114 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR J 114 " -0.048 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1654 2.79 - 3.32: 7696 3.32 - 3.85: 14998 3.85 - 4.37: 17613 4.37 - 4.90: 32309 Nonbonded interactions: 74270 Sorted by model distance: nonbonded pdb=" N SER J 112 " pdb=" OG SER K 112 " model vdw 2.263 3.120 nonbonded pdb=" N SER A 112 " pdb=" OG SER B 112 " model vdw 2.271 3.120 nonbonded pdb=" N SER I 112 " pdb=" OG SER J 112 " model vdw 2.274 3.120 nonbonded pdb=" N SER E 112 " pdb=" OG SER F 112 " model vdw 2.280 3.120 nonbonded pdb=" N SER B 112 " pdb=" OG SER C 112 " model vdw 2.312 3.120 ... (remaining 74265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.820 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 8096 Z= 0.580 Angle : 1.132 9.773 11000 Z= 0.727 Chirality : 0.084 0.379 1287 Planarity : 0.006 0.049 1353 Dihedral : 12.171 54.980 2871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % 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 are not related in a simple way. whole: -3.05 (0.22), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 34 TYR 0.091 0.009 TYR A 114 PHE 0.075 0.006 PHE K 64 TRP 0.014 0.005 TRP E 79 HIS 0.037 0.004 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00882 ( 8096) covalent geometry : angle 1.13161 (11000) hydrogen bonds : bond 0.19078 ( 192) hydrogen bonds : angle 9.25003 ( 576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9068 (mttt) cc_final: 0.8484 (mtpm) REVERT: A 34 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8153 (tpp80) REVERT: A 63 GLU cc_start: 0.8662 (pt0) cc_final: 0.8199 (pp20) REVERT: A 70 LYS cc_start: 0.9197 (tttt) cc_final: 0.8978 (tppp) REVERT: A 90 HIS cc_start: 0.8324 (m90) cc_final: 0.8116 (m90) REVERT: A 104 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: B 15 LYS cc_start: 0.8779 (mttt) cc_final: 0.8126 (mtpp) REVERT: B 34 ARG cc_start: 0.8540 (ttt180) cc_final: 0.8034 (tpp80) REVERT: B 90 HIS cc_start: 0.8469 (m90) cc_final: 0.8046 (m90) REVERT: C 15 LYS cc_start: 0.8955 (mttt) cc_final: 0.8266 (mtpp) REVERT: C 72 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 90 HIS cc_start: 0.8443 (m90) cc_final: 0.8112 (m90) REVERT: D 15 LYS cc_start: 0.8720 (mttt) cc_final: 0.8294 (ttmm) REVERT: D 34 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8443 (tpp80) REVERT: D 72 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7017 (mt-10) REVERT: D 80 LYS cc_start: 0.9076 (tttt) cc_final: 0.8859 (tttp) REVERT: D 90 HIS cc_start: 0.8505 (m90) cc_final: 0.8126 (m90) REVERT: E 15 LYS cc_start: 0.8968 (mttt) cc_final: 0.8308 (mtpp) REVERT: E 21 ARG cc_start: 0.8390 (tpt-90) cc_final: 0.8146 (tpp80) REVERT: E 34 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8433 (tpp80) REVERT: E 69 TYR cc_start: 0.8737 (m-80) cc_final: 0.8423 (m-80) REVERT: F 15 LYS cc_start: 0.8660 (mttt) cc_final: 0.8116 (ttmm) REVERT: F 21 ARG cc_start: 0.8401 (tpt-90) cc_final: 0.8152 (tpp80) REVERT: F 34 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8352 (tpp80) REVERT: F 80 LYS cc_start: 0.9055 (tttt) cc_final: 0.8833 (tttm) REVERT: G 15 LYS cc_start: 0.9048 (mttt) cc_final: 0.8449 (ttmm) REVERT: G 18 ASP cc_start: 0.8566 (m-30) cc_final: 0.8320 (m-30) REVERT: G 34 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8339 (tpp80) REVERT: G 63 GLU cc_start: 0.8441 (pt0) cc_final: 0.7899 (pm20) REVERT: G 90 HIS cc_start: 0.8552 (m90) cc_final: 0.8232 (m170) REVERT: G 99 ASP cc_start: 0.8518 (t0) cc_final: 0.8237 (t70) REVERT: H 15 LYS cc_start: 0.8885 (mttt) cc_final: 0.8233 (ttmm) REVERT: H 34 ARG cc_start: 0.8720 (ttt180) cc_final: 0.8378 (tpp80) REVERT: H 63 GLU cc_start: 0.8684 (pt0) cc_final: 0.8083 (pm20) REVERT: H 70 LYS cc_start: 0.9256 (tttt) cc_final: 0.8896 (tppp) REVERT: H 90 HIS cc_start: 0.8457 (m90) cc_final: 0.8120 (m90) REVERT: I 15 LYS cc_start: 0.8880 (mttt) cc_final: 0.8356 (ttmm) REVERT: I 34 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8247 (tpp80) REVERT: I 80 LYS cc_start: 0.9178 (tttt) cc_final: 0.8944 (tttm) REVERT: I 100 SER cc_start: 0.8866 (t) cc_final: 0.8632 (p) REVERT: J 15 LYS cc_start: 0.8921 (mttt) cc_final: 0.8381 (ttmm) REVERT: J 34 ARG cc_start: 0.8652 (ttt180) cc_final: 0.8160 (tpp80) REVERT: J 63 GLU cc_start: 0.8685 (pt0) cc_final: 0.8435 (pt0) REVERT: J 84 ILE cc_start: 0.9426 (mt) cc_final: 0.9050 (pp) REVERT: J 100 SER cc_start: 0.8953 (t) cc_final: 0.8749 (p) REVERT: K 15 LYS cc_start: 0.8656 (mttt) cc_final: 0.8114 (ttmm) REVERT: K 27 ASN cc_start: 0.8796 (m-40) cc_final: 0.8539 (m-40) REVERT: K 80 LYS cc_start: 0.9062 (tttt) cc_final: 0.8836 (tttm) REVERT: K 84 ILE cc_start: 0.9476 (mt) cc_final: 0.9259 (pp) REVERT: K 90 HIS cc_start: 0.8669 (m90) cc_final: 0.8234 (m90) REVERT: K 100 SER cc_start: 0.8985 (t) cc_final: 0.8768 (p) outliers start: 1 outliers final: 1 residues processed: 393 average time/residue: 0.6222 time to fit residues: 256.8185 Evaluate side-chains 336 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.072882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.054074 restraints weight = 17159.201| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.67 r_work: 0.3353 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8096 Z= 0.207 Angle : 0.784 8.206 11000 Z= 0.408 Chirality : 0.054 0.145 1287 Planarity : 0.005 0.045 1353 Dihedral : 5.992 24.907 1091 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.08 % Allowed : 20.40 % Favored : 75.52 % 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 are not related in a simple way. whole: -2.78 (0.22), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 104 TYR 0.024 0.003 TYR K 114 PHE 0.017 0.001 PHE K 64 TRP 0.006 0.001 TRP A 79 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8096) covalent geometry : angle 0.78419 (11000) hydrogen bonds : bond 0.04704 ( 192) hydrogen bonds : angle 5.57790 ( 576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 357 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8453 (tmm) cc_final: 0.8195 (tmm) REVERT: A 15 LYS cc_start: 0.8912 (mttt) cc_final: 0.8251 (mtpm) REVERT: A 18 ASP cc_start: 0.8506 (m-30) cc_final: 0.8261 (m-30) REVERT: A 34 ARG cc_start: 0.8695 (ttt180) cc_final: 0.7993 (tpp80) REVERT: A 63 GLU cc_start: 0.8882 (pt0) cc_final: 0.8225 (pp20) REVERT: A 66 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 88 HIS cc_start: 0.9258 (t-90) cc_final: 0.9012 (t-90) REVERT: A 89 GLU cc_start: 0.7323 (mp0) cc_final: 0.7089 (pm20) REVERT: A 90 HIS cc_start: 0.8247 (m90) cc_final: 0.7892 (m90) REVERT: A 104 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7865 (mtt-85) REVERT: A 106 THR cc_start: 0.9254 (m) cc_final: 0.8915 (p) REVERT: B 13 MET cc_start: 0.7889 (tmm) cc_final: 0.7508 (tmm) REVERT: B 15 LYS cc_start: 0.8652 (mttt) cc_final: 0.8166 (mtpp) REVERT: B 21 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7926 (tpp80) REVERT: B 34 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8110 (tpp80) REVERT: B 66 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 80 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8651 (ttpt) REVERT: B 90 HIS cc_start: 0.8162 (m90) cc_final: 0.7774 (m90) REVERT: B 92 GLU cc_start: 0.7062 (mp0) cc_final: 0.6757 (mp0) REVERT: B 104 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7980 (ttm110) REVERT: C 30 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7808 (tmm) REVERT: C 63 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: C 66 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: C 90 HIS cc_start: 0.8258 (m90) cc_final: 0.8010 (m90) REVERT: D 13 MET cc_start: 0.7981 (tmm) cc_final: 0.7288 (tmm) REVERT: D 15 LYS cc_start: 0.8551 (mttt) cc_final: 0.7910 (mtpm) REVERT: D 21 ARG cc_start: 0.8493 (mmm160) cc_final: 0.8270 (mmm160) REVERT: D 34 ARG cc_start: 0.8998 (ttt180) cc_final: 0.8470 (tpp80) REVERT: D 63 GLU cc_start: 0.7864 (pm20) cc_final: 0.7613 (pm20) REVERT: D 70 LYS cc_start: 0.8936 (tttp) cc_final: 0.8697 (tttp) REVERT: D 72 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7587 (mt-10) REVERT: D 80 LYS cc_start: 0.8922 (tttt) cc_final: 0.8608 (tttm) REVERT: D 90 HIS cc_start: 0.8441 (m90) cc_final: 0.8208 (m-70) REVERT: D 99 ASP cc_start: 0.8971 (t70) cc_final: 0.8761 (t70) REVERT: D 104 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8120 (ttm110) REVERT: D 116 TYR cc_start: 0.9448 (m-80) cc_final: 0.9155 (m-80) REVERT: E 13 MET cc_start: 0.8196 (tmm) cc_final: 0.7419 (tmm) REVERT: E 15 LYS cc_start: 0.8776 (mttt) cc_final: 0.8203 (mttm) REVERT: E 21 ARG cc_start: 0.8427 (tpt-90) cc_final: 0.7943 (mmm160) REVERT: E 26 ILE cc_start: 0.9152 (mt) cc_final: 0.8893 (mp) REVERT: E 30 MET cc_start: 0.7345 (tmm) cc_final: 0.6999 (tmm) REVERT: E 34 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8365 (tpp80) REVERT: E 66 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7697 (tm-30) REVERT: E 70 LYS cc_start: 0.8972 (tttt) cc_final: 0.8404 (ttpp) REVERT: E 104 ARG cc_start: 0.8677 (ttm110) cc_final: 0.8201 (mtm-85) REVERT: F 13 MET cc_start: 0.7892 (tmm) cc_final: 0.7198 (tmm) REVERT: F 15 LYS cc_start: 0.8604 (mttt) cc_final: 0.8018 (mtpm) REVERT: F 21 ARG cc_start: 0.8591 (tpt-90) cc_final: 0.8080 (mmm160) REVERT: F 30 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7936 (tmm) REVERT: F 34 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8376 (tpp80) REVERT: F 35 LYS cc_start: 0.9267 (ttmt) cc_final: 0.8901 (ttmm) REVERT: F 62 GLU cc_start: 0.8144 (pm20) cc_final: 0.7845 (pm20) REVERT: F 63 GLU cc_start: 0.7937 (pm20) cc_final: 0.7169 (pm20) REVERT: F 80 LYS cc_start: 0.8926 (tttt) cc_final: 0.8619 (tttm) REVERT: G 13 MET cc_start: 0.8276 (tmm) cc_final: 0.7724 (tmm) REVERT: G 15 LYS cc_start: 0.8784 (mttt) cc_final: 0.8287 (mttm) REVERT: G 21 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8223 (tpp80) REVERT: G 34 ARG cc_start: 0.8822 (ttt180) cc_final: 0.8233 (tpp80) REVERT: G 63 GLU cc_start: 0.8503 (pt0) cc_final: 0.7631 (pm20) REVERT: G 69 TYR cc_start: 0.9127 (m-80) cc_final: 0.8910 (m-80) REVERT: G 104 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8099 (ttm110) REVERT: H 15 LYS cc_start: 0.8582 (mttt) cc_final: 0.8001 (ttmm) REVERT: H 34 ARG cc_start: 0.9038 (ttt180) cc_final: 0.8421 (tpp80) REVERT: H 62 GLU cc_start: 0.7798 (mp0) cc_final: 0.7453 (mp0) REVERT: H 63 GLU cc_start: 0.8655 (pt0) cc_final: 0.7909 (pm20) REVERT: H 66 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7661 (tm-30) REVERT: H 90 HIS cc_start: 0.8372 (m90) cc_final: 0.7966 (m90) REVERT: I 13 MET cc_start: 0.8009 (tmm) cc_final: 0.7495 (tmm) REVERT: I 15 LYS cc_start: 0.8555 (mttt) cc_final: 0.7938 (ttmm) REVERT: I 34 ARG cc_start: 0.8748 (ttt180) cc_final: 0.8424 (tpp80) REVERT: I 80 LYS cc_start: 0.8865 (tttt) cc_final: 0.8514 (tttm) REVERT: I 89 GLU cc_start: 0.7826 (mp0) cc_final: 0.7622 (pm20) REVERT: I 99 ASP cc_start: 0.8929 (t0) cc_final: 0.8290 (t70) REVERT: I 100 SER cc_start: 0.8746 (t) cc_final: 0.8447 (p) REVERT: I 104 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7815 (ttm110) REVERT: J 15 LYS cc_start: 0.8537 (mttt) cc_final: 0.7892 (ttmm) REVERT: J 21 ARG cc_start: 0.8346 (mmm160) cc_final: 0.8106 (mmm160) REVERT: J 34 ARG cc_start: 0.8553 (ttt180) cc_final: 0.7833 (tpp80) REVERT: J 63 GLU cc_start: 0.8528 (pt0) cc_final: 0.8103 (pt0) REVERT: J 66 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7772 (tm-30) REVERT: J 72 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8515 (mm-30) REVERT: J 84 ILE cc_start: 0.9326 (mt) cc_final: 0.8758 (pp) REVERT: J 100 SER cc_start: 0.8965 (t) cc_final: 0.8612 (p) REVERT: K 15 LYS cc_start: 0.8508 (mttt) cc_final: 0.7852 (mtpm) REVERT: K 21 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8190 (mtp85) REVERT: K 30 MET cc_start: 0.7949 (ppp) cc_final: 0.7710 (ppp) REVERT: K 62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7775 (mp0) REVERT: K 63 GLU cc_start: 0.8675 (pt0) cc_final: 0.8377 (pt0) REVERT: K 80 LYS cc_start: 0.8939 (tttt) cc_final: 0.8537 (tttm) REVERT: K 84 ILE cc_start: 0.9531 (mt) cc_final: 0.9316 (mp) REVERT: K 90 HIS cc_start: 0.8666 (m90) cc_final: 0.8296 (m90) REVERT: K 99 ASP cc_start: 0.8564 (t0) cc_final: 0.8116 (t70) REVERT: K 100 SER cc_start: 0.9049 (t) cc_final: 0.8772 (p) REVERT: K 118 THR cc_start: 0.9198 (m) cc_final: 0.8840 (p) outliers start: 35 outliers final: 5 residues processed: 369 average time/residue: 0.6927 time to fit residues: 267.5737 Evaluate side-chains 348 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 338 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain J residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.068125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.048527 restraints weight = 17859.470| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.63 r_work: 0.3097 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.058 8096 Z= 0.445 Angle : 0.835 8.970 11000 Z= 0.443 Chirality : 0.055 0.154 1287 Planarity : 0.005 0.040 1353 Dihedral : 6.182 25.467 1089 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.43 % Allowed : 21.79 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 104 TYR 0.022 0.003 TYR K 105 PHE 0.026 0.002 PHE K 64 TRP 0.010 0.002 TRP A 79 HIS 0.008 0.003 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00951 ( 8096) covalent geometry : angle 0.83550 (11000) hydrogen bonds : bond 0.04486 ( 192) hydrogen bonds : angle 5.08995 ( 576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8682 (ttt180) cc_final: 0.8178 (tpp80) REVERT: A 63 GLU cc_start: 0.8849 (pt0) cc_final: 0.8249 (pp20) REVERT: A 66 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 70 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8734 (tppp) REVERT: A 90 HIS cc_start: 0.8208 (m90) cc_final: 0.7988 (m90) REVERT: A 104 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7153 (mtm-85) REVERT: B 13 MET cc_start: 0.7933 (tmm) cc_final: 0.7613 (tmm) REVERT: B 15 LYS cc_start: 0.8593 (mttt) cc_final: 0.7915 (mtpm) REVERT: B 34 ARG cc_start: 0.8787 (ttt180) cc_final: 0.8208 (tpp80) REVERT: B 62 GLU cc_start: 0.8018 (mp0) cc_final: 0.7417 (mp0) REVERT: B 66 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7558 (tm-30) REVERT: B 80 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8672 (ttpt) REVERT: B 90 HIS cc_start: 0.8232 (m90) cc_final: 0.7857 (m90) REVERT: B 99 ASP cc_start: 0.9123 (t70) cc_final: 0.8872 (t70) REVERT: B 104 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: C 15 LYS cc_start: 0.8701 (mttt) cc_final: 0.8162 (mtpm) REVERT: C 30 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7614 (tmm) REVERT: C 63 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: C 66 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: C 89 GLU cc_start: 0.7874 (mp0) cc_final: 0.7325 (pm20) REVERT: C 90 HIS cc_start: 0.8424 (m90) cc_final: 0.8216 (m90) REVERT: D 13 MET cc_start: 0.8120 (tmm) cc_final: 0.7744 (tmm) REVERT: D 21 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8333 (mmm160) REVERT: D 34 ARG cc_start: 0.9054 (ttt180) cc_final: 0.8458 (tpp80) REVERT: D 62 GLU cc_start: 0.7906 (mp0) cc_final: 0.7685 (mp0) REVERT: D 63 GLU cc_start: 0.7818 (pm20) cc_final: 0.7618 (pm20) REVERT: D 66 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 80 LYS cc_start: 0.8963 (tttt) cc_final: 0.8624 (tttm) REVERT: D 89 GLU cc_start: 0.8295 (mp0) cc_final: 0.7878 (mp0) REVERT: D 104 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.8195 (ttm110) REVERT: E 13 MET cc_start: 0.8298 (tmm) cc_final: 0.7948 (tmm) REVERT: E 21 ARG cc_start: 0.8469 (tpt-90) cc_final: 0.7964 (mmm160) REVERT: E 26 ILE cc_start: 0.9154 (mt) cc_final: 0.8882 (mp) REVERT: E 30 MET cc_start: 0.7825 (tmm) cc_final: 0.7254 (tmm) REVERT: E 34 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8427 (tpp80) REVERT: E 66 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7819 (tm-30) REVERT: E 70 LYS cc_start: 0.9154 (tttt) cc_final: 0.8886 (ttpp) REVERT: E 72 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: E 89 GLU cc_start: 0.7600 (mp0) cc_final: 0.7399 (mp0) REVERT: F 13 MET cc_start: 0.8098 (tmm) cc_final: 0.7583 (tmm) REVERT: F 15 LYS cc_start: 0.8775 (mttt) cc_final: 0.8260 (mtpm) REVERT: F 18 ASP cc_start: 0.8959 (m-30) cc_final: 0.8696 (m-30) REVERT: F 21 ARG cc_start: 0.8742 (tpt-90) cc_final: 0.8424 (mtp-110) REVERT: F 30 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: F 34 ARG cc_start: 0.9015 (ttt180) cc_final: 0.8320 (tpp80) REVERT: F 35 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8886 (ttmm) REVERT: F 62 GLU cc_start: 0.8176 (pm20) cc_final: 0.7919 (pm20) REVERT: F 63 GLU cc_start: 0.7910 (pm20) cc_final: 0.7232 (pm20) REVERT: F 66 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7763 (tm-30) REVERT: F 80 LYS cc_start: 0.8978 (tttt) cc_final: 0.8666 (tttp) REVERT: F 84 ILE cc_start: 0.9293 (mm) cc_final: 0.8828 (pp) REVERT: G 13 MET cc_start: 0.8559 (tmm) cc_final: 0.8291 (tmm) REVERT: G 34 ARG cc_start: 0.8830 (ttt180) cc_final: 0.8224 (tpp80) REVERT: G 63 GLU cc_start: 0.8542 (pt0) cc_final: 0.7770 (pm20) REVERT: G 66 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7779 (tm-30) REVERT: G 70 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8965 (ttpp) REVERT: G 72 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8135 (mp0) REVERT: G 104 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8198 (ttm110) REVERT: H 15 LYS cc_start: 0.8668 (mttt) cc_final: 0.8104 (mtpp) REVERT: H 34 ARG cc_start: 0.8993 (ttt180) cc_final: 0.8388 (tpp80) REVERT: H 62 GLU cc_start: 0.8135 (mp0) cc_final: 0.7503 (mp0) REVERT: H 63 GLU cc_start: 0.8769 (pt0) cc_final: 0.7996 (pm20) REVERT: H 66 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7957 (tm-30) REVERT: H 72 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8806 (mt-10) REVERT: H 90 HIS cc_start: 0.8321 (m90) cc_final: 0.7965 (m90) REVERT: I 13 MET cc_start: 0.8089 (tmm) cc_final: 0.7689 (tmm) REVERT: I 15 LYS cc_start: 0.8815 (mttt) cc_final: 0.8098 (ttmm) REVERT: I 34 ARG cc_start: 0.8759 (ttt180) cc_final: 0.8381 (tpp80) REVERT: I 63 GLU cc_start: 0.8576 (pt0) cc_final: 0.8351 (pt0) REVERT: I 70 LYS cc_start: 0.9395 (ttmm) cc_final: 0.8988 (ttpp) REVERT: I 80 LYS cc_start: 0.8896 (tttt) cc_final: 0.8529 (tttm) REVERT: I 100 SER cc_start: 0.8812 (t) cc_final: 0.8516 (p) REVERT: I 104 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7938 (ttm110) REVERT: J 13 MET cc_start: 0.8384 (tmm) cc_final: 0.7724 (tmm) REVERT: J 15 LYS cc_start: 0.8603 (mttt) cc_final: 0.7868 (mtpp) REVERT: J 21 ARG cc_start: 0.8448 (mmm160) cc_final: 0.8203 (mmm160) REVERT: J 34 ARG cc_start: 0.8591 (ttt180) cc_final: 0.8052 (tpp80) REVERT: J 35 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8711 (ttmm) REVERT: J 61 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: J 62 GLU cc_start: 0.8327 (mp0) cc_final: 0.8071 (mp0) REVERT: J 63 GLU cc_start: 0.8632 (pt0) cc_final: 0.8222 (pt0) REVERT: J 66 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7647 (tm-30) REVERT: J 84 ILE cc_start: 0.9294 (mt) cc_final: 0.8765 (pp) REVERT: J 100 SER cc_start: 0.9029 (t) cc_final: 0.8705 (p) REVERT: K 13 MET cc_start: 0.8090 (tmm) cc_final: 0.7588 (tmt) REVERT: K 15 LYS cc_start: 0.8488 (mttt) cc_final: 0.7886 (mtpm) REVERT: K 21 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8238 (mtp85) REVERT: K 62 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7561 (mp0) REVERT: K 63 GLU cc_start: 0.8702 (pt0) cc_final: 0.8449 (pt0) REVERT: K 80 LYS cc_start: 0.8951 (tttt) cc_final: 0.8544 (tttp) REVERT: K 90 HIS cc_start: 0.8631 (m90) cc_final: 0.8303 (m90) REVERT: K 99 ASP cc_start: 0.8588 (t0) cc_final: 0.8260 (t70) REVERT: K 100 SER cc_start: 0.9091 (t) cc_final: 0.8841 (p) REVERT: K 118 THR cc_start: 0.9185 (m) cc_final: 0.8775 (p) outliers start: 38 outliers final: 18 residues processed: 342 average time/residue: 0.7357 time to fit residues: 262.7408 Evaluate side-chains 342 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN D 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.071921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052371 restraints weight = 17412.919| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.69 r_work: 0.3291 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8096 Z= 0.162 Angle : 0.755 9.498 11000 Z= 0.385 Chirality : 0.051 0.143 1287 Planarity : 0.004 0.040 1353 Dihedral : 5.793 23.753 1089 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.01 % Allowed : 24.01 % Favored : 70.98 % 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 are not related in a simple way. whole: -2.74 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 104 TYR 0.022 0.002 TYR E 105 PHE 0.023 0.001 PHE K 64 TRP 0.003 0.001 TRP A 79 HIS 0.005 0.002 HIS G 88 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8096) covalent geometry : angle 0.75540 (11000) hydrogen bonds : bond 0.03316 ( 192) hydrogen bonds : angle 5.00025 ( 576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8743 (ttt180) cc_final: 0.8198 (tpp80) REVERT: A 62 GLU cc_start: 0.7617 (mp0) cc_final: 0.7242 (mp0) REVERT: A 63 GLU cc_start: 0.8910 (pt0) cc_final: 0.8166 (pp20) REVERT: A 66 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 70 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8836 (tppp) REVERT: A 89 GLU cc_start: 0.7560 (pm20) cc_final: 0.6418 (pm20) REVERT: A 90 HIS cc_start: 0.8405 (m90) cc_final: 0.7980 (m90) REVERT: A 92 GLU cc_start: 0.7695 (mp0) cc_final: 0.7457 (mp0) REVERT: A 104 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7230 (mtm-85) REVERT: A 106 THR cc_start: 0.9197 (m) cc_final: 0.8828 (t) REVERT: B 13 MET cc_start: 0.8042 (tmm) cc_final: 0.7767 (tmm) REVERT: B 15 LYS cc_start: 0.8665 (mttt) cc_final: 0.7923 (mtpm) REVERT: B 34 ARG cc_start: 0.8795 (ttt180) cc_final: 0.8155 (tpp80) REVERT: B 35 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8867 (mtpp) REVERT: B 62 GLU cc_start: 0.7855 (mp0) cc_final: 0.7265 (mp0) REVERT: B 63 GLU cc_start: 0.7776 (pm20) cc_final: 0.7572 (pm20) REVERT: B 66 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 69 TYR cc_start: 0.9416 (m-80) cc_final: 0.9205 (m-80) REVERT: B 80 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8655 (ttpt) REVERT: B 90 HIS cc_start: 0.8282 (m90) cc_final: 0.7869 (m90) REVERT: B 92 GLU cc_start: 0.7191 (mp0) cc_final: 0.6950 (mp0) REVERT: B 99 ASP cc_start: 0.9084 (t70) cc_final: 0.8866 (t70) REVERT: B 104 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: C 15 LYS cc_start: 0.8658 (mttt) cc_final: 0.8127 (mtpm) REVERT: C 18 ASP cc_start: 0.8849 (m-30) cc_final: 0.8369 (m-30) REVERT: C 63 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7370 (pm20) REVERT: C 89 GLU cc_start: 0.7880 (mp0) cc_final: 0.7185 (pm20) REVERT: C 90 HIS cc_start: 0.8568 (m90) cc_final: 0.8273 (m90) REVERT: D 13 MET cc_start: 0.8074 (tmm) cc_final: 0.7633 (tmm) REVERT: D 15 LYS cc_start: 0.8570 (mttt) cc_final: 0.8037 (mtpm) REVERT: D 34 ARG cc_start: 0.9048 (ttt180) cc_final: 0.8434 (tpp80) REVERT: D 62 GLU cc_start: 0.7956 (mp0) cc_final: 0.7483 (mp0) REVERT: D 66 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7770 (tm-30) REVERT: D 80 LYS cc_start: 0.8987 (tttt) cc_final: 0.8630 (tttm) REVERT: D 89 GLU cc_start: 0.8346 (mp0) cc_final: 0.8129 (mp0) REVERT: D 104 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8289 (mtm-85) REVERT: E 13 MET cc_start: 0.8342 (tmm) cc_final: 0.7971 (tmm) REVERT: E 21 ARG cc_start: 0.8484 (tpt-90) cc_final: 0.8009 (mmm160) REVERT: E 30 MET cc_start: 0.7902 (tmm) cc_final: 0.7457 (tmm) REVERT: E 34 ARG cc_start: 0.8987 (ttt180) cc_final: 0.8385 (tpp80) REVERT: E 66 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 70 LYS cc_start: 0.9178 (tttt) cc_final: 0.8924 (ttpp) REVERT: E 72 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: F 13 MET cc_start: 0.8147 (tmm) cc_final: 0.7607 (tmm) REVERT: F 15 LYS cc_start: 0.8772 (mttt) cc_final: 0.8176 (mtpm) REVERT: F 18 ASP cc_start: 0.8960 (m-30) cc_final: 0.8628 (m-30) REVERT: F 21 ARG cc_start: 0.8623 (tpt-90) cc_final: 0.8326 (mtp-110) REVERT: F 30 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7861 (tmm) REVERT: F 34 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8334 (tpp80) REVERT: F 62 GLU cc_start: 0.8121 (pm20) cc_final: 0.7601 (pm20) REVERT: F 63 GLU cc_start: 0.7921 (pm20) cc_final: 0.7192 (pm20) REVERT: F 66 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7717 (tm-30) REVERT: F 69 TYR cc_start: 0.9295 (m-80) cc_final: 0.9063 (m-80) REVERT: F 80 LYS cc_start: 0.8957 (tttt) cc_final: 0.8641 (tttp) REVERT: G 13 MET cc_start: 0.8632 (tmm) cc_final: 0.7955 (tmm) REVERT: G 15 LYS cc_start: 0.8960 (mttt) cc_final: 0.8275 (mttp) REVERT: G 30 MET cc_start: 0.7976 (tmm) cc_final: 0.7018 (tmm) REVERT: G 34 ARG cc_start: 0.8881 (ttt180) cc_final: 0.8296 (tpp80) REVERT: G 61 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: G 63 GLU cc_start: 0.8538 (pt0) cc_final: 0.7610 (pm20) REVERT: G 66 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7621 (tm-30) REVERT: G 104 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8105 (ttm110) REVERT: H 15 LYS cc_start: 0.8667 (mttt) cc_final: 0.8136 (mtpp) REVERT: H 30 MET cc_start: 0.8457 (mtp) cc_final: 0.8129 (tmm) REVERT: H 34 ARG cc_start: 0.8982 (ttt180) cc_final: 0.8345 (tpp80) REVERT: H 62 GLU cc_start: 0.8205 (mp0) cc_final: 0.7441 (mp0) REVERT: H 63 GLU cc_start: 0.8708 (pt0) cc_final: 0.7971 (pm20) REVERT: H 66 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7697 (tm-30) REVERT: H 90 HIS cc_start: 0.8452 (m90) cc_final: 0.8166 (m90) REVERT: I 13 MET cc_start: 0.8015 (tmm) cc_final: 0.7554 (tmm) REVERT: I 15 LYS cc_start: 0.8679 (mttt) cc_final: 0.7965 (ttmm) REVERT: I 18 ASP cc_start: 0.8794 (m-30) cc_final: 0.8342 (m-30) REVERT: I 34 ARG cc_start: 0.8795 (ttt180) cc_final: 0.8410 (tpp80) REVERT: I 63 GLU cc_start: 0.8496 (pt0) cc_final: 0.8267 (pt0) REVERT: I 70 LYS cc_start: 0.9389 (ttmm) cc_final: 0.9084 (ttpp) REVERT: I 80 LYS cc_start: 0.8876 (tttt) cc_final: 0.8511 (tttp) REVERT: I 99 ASP cc_start: 0.8815 (t0) cc_final: 0.8213 (t70) REVERT: I 100 SER cc_start: 0.8789 (t) cc_final: 0.8481 (p) REVERT: I 104 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7825 (ttm110) REVERT: J 13 MET cc_start: 0.8422 (tmm) cc_final: 0.7909 (tmm) REVERT: J 34 ARG cc_start: 0.8652 (ttt180) cc_final: 0.7955 (tpp80) REVERT: J 35 LYS cc_start: 0.8980 (ttmm) cc_final: 0.8739 (ttmm) REVERT: J 61 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: J 62 GLU cc_start: 0.8461 (mp0) cc_final: 0.8029 (mp0) REVERT: J 63 GLU cc_start: 0.8621 (pt0) cc_final: 0.8176 (pt0) REVERT: J 66 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7482 (tm-30) REVERT: J 84 ILE cc_start: 0.9343 (mt) cc_final: 0.8822 (pp) REVERT: J 100 SER cc_start: 0.8947 (t) cc_final: 0.8559 (p) REVERT: K 13 MET cc_start: 0.8043 (tmm) cc_final: 0.7808 (tmm) REVERT: K 15 LYS cc_start: 0.8515 (mttt) cc_final: 0.7932 (mtpm) REVERT: K 21 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8333 (mtp85) REVERT: K 58 LEU cc_start: 0.8792 (mt) cc_final: 0.8519 (tp) REVERT: K 62 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7791 (mp0) REVERT: K 63 GLU cc_start: 0.8776 (pt0) cc_final: 0.8492 (pt0) REVERT: K 66 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8151 (tm-30) REVERT: K 80 LYS cc_start: 0.8904 (tttt) cc_final: 0.8516 (tttp) REVERT: K 90 HIS cc_start: 0.8798 (m90) cc_final: 0.8595 (m90) REVERT: K 99 ASP cc_start: 0.8520 (t0) cc_final: 0.8211 (t70) REVERT: K 118 THR cc_start: 0.9233 (m) cc_final: 0.8873 (p) outliers start: 43 outliers final: 16 residues processed: 365 average time/residue: 0.6531 time to fit residues: 249.5687 Evaluate side-chains 354 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 66 optimal weight: 0.0770 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.070266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.051903 restraints weight = 17348.020| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 3.64 r_work: 0.3305 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8096 Z= 0.192 Angle : 0.771 9.651 11000 Z= 0.390 Chirality : 0.052 0.173 1287 Planarity : 0.005 0.047 1353 Dihedral : 5.724 23.317 1089 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.01 % Allowed : 25.52 % Favored : 69.46 % 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 are not related in a simple way. whole: -2.79 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 104 TYR 0.021 0.002 TYR K 114 PHE 0.026 0.002 PHE K 64 TRP 0.003 0.001 TRP A 79 HIS 0.007 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8096) covalent geometry : angle 0.77148 (11000) hydrogen bonds : bond 0.03027 ( 192) hydrogen bonds : angle 4.91115 ( 576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 345 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8789 (ttt180) cc_final: 0.8216 (tpp80) REVERT: A 62 GLU cc_start: 0.7650 (mp0) cc_final: 0.7365 (mp0) REVERT: A 63 GLU cc_start: 0.8898 (pt0) cc_final: 0.8174 (pp20) REVERT: A 66 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 70 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8895 (tppp) REVERT: A 89 GLU cc_start: 0.7864 (pm20) cc_final: 0.7310 (pm20) REVERT: A 90 HIS cc_start: 0.8420 (m90) cc_final: 0.8007 (m90) REVERT: A 104 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7731 (mtt90) REVERT: A 106 THR cc_start: 0.9195 (m) cc_final: 0.8826 (t) REVERT: B 13 MET cc_start: 0.8066 (tmm) cc_final: 0.7638 (tmm) REVERT: B 15 LYS cc_start: 0.8663 (mttt) cc_final: 0.7945 (mtpm) REVERT: B 18 ASP cc_start: 0.9006 (m-30) cc_final: 0.8337 (m-30) REVERT: B 34 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8131 (tpp80) REVERT: B 35 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8868 (mtpp) REVERT: B 62 GLU cc_start: 0.7873 (mp0) cc_final: 0.7340 (mp0) REVERT: B 66 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 69 TYR cc_start: 0.9419 (m-80) cc_final: 0.9200 (m-80) REVERT: B 80 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8660 (ttpt) REVERT: B 90 HIS cc_start: 0.8365 (m90) cc_final: 0.7972 (m90) REVERT: B 99 ASP cc_start: 0.9057 (t70) cc_final: 0.8853 (t70) REVERT: C 15 LYS cc_start: 0.8628 (mttt) cc_final: 0.8112 (mtpm) REVERT: C 18 ASP cc_start: 0.8889 (m-30) cc_final: 0.8487 (m-30) REVERT: C 30 MET cc_start: 0.8419 (ttm) cc_final: 0.8027 (tmm) REVERT: C 35 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8885 (ttmm) REVERT: C 62 GLU cc_start: 0.8050 (mp0) cc_final: 0.7754 (mp0) REVERT: C 63 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: C 66 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: C 89 GLU cc_start: 0.7933 (mp0) cc_final: 0.7542 (mp0) REVERT: C 90 HIS cc_start: 0.8590 (m90) cc_final: 0.8227 (m90) REVERT: D 13 MET cc_start: 0.8099 (tmm) cc_final: 0.7616 (tmm) REVERT: D 15 LYS cc_start: 0.8629 (mttt) cc_final: 0.8055 (mtpm) REVERT: D 34 ARG cc_start: 0.9047 (ttt180) cc_final: 0.8424 (tpp80) REVERT: D 62 GLU cc_start: 0.8015 (mp0) cc_final: 0.7560 (mp0) REVERT: D 63 GLU cc_start: 0.7894 (pm20) cc_final: 0.7518 (pm20) REVERT: D 66 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7846 (tm-30) REVERT: D 80 LYS cc_start: 0.8974 (tttt) cc_final: 0.8630 (tttm) REVERT: D 104 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8237 (mtm-85) REVERT: D 116 TYR cc_start: 0.9447 (m-80) cc_final: 0.9191 (m-80) REVERT: E 13 MET cc_start: 0.8365 (tmm) cc_final: 0.8022 (tmm) REVERT: E 21 ARG cc_start: 0.8381 (tpt-90) cc_final: 0.8081 (mmm160) REVERT: E 30 MET cc_start: 0.8071 (tmm) cc_final: 0.7556 (tmm) REVERT: E 34 ARG cc_start: 0.8937 (ttt180) cc_final: 0.8412 (tpp80) REVERT: E 62 GLU cc_start: 0.8465 (pm20) cc_final: 0.8151 (pm20) REVERT: E 66 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 72 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: F 13 MET cc_start: 0.8178 (tmm) cc_final: 0.7778 (tmm) REVERT: F 15 LYS cc_start: 0.8743 (mttt) cc_final: 0.8076 (mtpm) REVERT: F 18 ASP cc_start: 0.8902 (m-30) cc_final: 0.8542 (m-30) REVERT: F 30 MET cc_start: 0.8295 (ttm) cc_final: 0.7837 (tmm) REVERT: F 34 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8300 (tpp80) REVERT: F 35 LYS cc_start: 0.9204 (ttpt) cc_final: 0.8895 (ttmm) REVERT: F 62 GLU cc_start: 0.8233 (pm20) cc_final: 0.7681 (pm20) REVERT: F 63 GLU cc_start: 0.7922 (pm20) cc_final: 0.7164 (pm20) REVERT: F 66 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7655 (tm-30) REVERT: F 80 LYS cc_start: 0.8955 (tttt) cc_final: 0.8643 (tttp) REVERT: F 89 GLU cc_start: 0.7725 (mp0) cc_final: 0.7255 (pm20) REVERT: G 13 MET cc_start: 0.8657 (tmm) cc_final: 0.7825 (tmm) REVERT: G 15 LYS cc_start: 0.8965 (mttt) cc_final: 0.8245 (mttm) REVERT: G 30 MET cc_start: 0.8064 (tmm) cc_final: 0.7168 (tmm) REVERT: G 34 ARG cc_start: 0.8916 (ttt180) cc_final: 0.8313 (tpp80) REVERT: G 63 GLU cc_start: 0.8518 (pt0) cc_final: 0.7525 (pm20) REVERT: G 66 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7450 (tm-30) REVERT: G 70 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9186 (ttpp) REVERT: G 89 GLU cc_start: 0.8145 (mp0) cc_final: 0.7857 (mp0) REVERT: H 15 LYS cc_start: 0.8696 (mttt) cc_final: 0.8147 (mtpp) REVERT: H 30 MET cc_start: 0.8396 (mtp) cc_final: 0.8086 (tmm) REVERT: H 34 ARG cc_start: 0.8962 (ttt180) cc_final: 0.8329 (tpp80) REVERT: H 62 GLU cc_start: 0.8308 (mp0) cc_final: 0.7785 (mp0) REVERT: H 63 GLU cc_start: 0.8746 (pt0) cc_final: 0.8050 (pm20) REVERT: H 66 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7703 (tm-30) REVERT: H 84 ILE cc_start: 0.9345 (mt) cc_final: 0.8848 (pp) REVERT: I 13 MET cc_start: 0.8058 (tmm) cc_final: 0.7581 (tmm) REVERT: I 15 LYS cc_start: 0.8755 (mttt) cc_final: 0.8109 (ttmm) REVERT: I 34 ARG cc_start: 0.8766 (ttt180) cc_final: 0.8378 (tpp80) REVERT: I 70 LYS cc_start: 0.9313 (ttmm) cc_final: 0.9053 (ttpp) REVERT: I 80 LYS cc_start: 0.8884 (tttt) cc_final: 0.8518 (tttm) REVERT: I 99 ASP cc_start: 0.8774 (t0) cc_final: 0.8234 (t70) REVERT: I 100 SER cc_start: 0.8799 (t) cc_final: 0.8528 (p) REVERT: I 104 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7836 (ttm110) REVERT: J 13 MET cc_start: 0.8422 (tmm) cc_final: 0.8127 (tmm) REVERT: J 15 LYS cc_start: 0.8637 (mttt) cc_final: 0.7900 (ttmm) REVERT: J 21 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8039 (mmm-85) REVERT: J 34 ARG cc_start: 0.8658 (ttt180) cc_final: 0.7955 (tpp80) REVERT: J 35 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8693 (ttmm) REVERT: J 63 GLU cc_start: 0.8637 (pt0) cc_final: 0.8346 (pt0) REVERT: J 66 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7593 (tm-30) REVERT: J 84 ILE cc_start: 0.9322 (mt) cc_final: 0.8805 (pp) REVERT: J 100 SER cc_start: 0.8926 (t) cc_final: 0.8533 (p) REVERT: K 13 MET cc_start: 0.8111 (tmm) cc_final: 0.7870 (tmm) REVERT: K 15 LYS cc_start: 0.8498 (mttt) cc_final: 0.7897 (mtpm) REVERT: K 21 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8350 (mtp85) REVERT: K 62 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7832 (mp0) REVERT: K 63 GLU cc_start: 0.8766 (pt0) cc_final: 0.8561 (pt0) REVERT: K 66 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8240 (tm-30) REVERT: K 80 LYS cc_start: 0.8897 (tttt) cc_final: 0.8503 (tttp) REVERT: K 99 ASP cc_start: 0.8490 (t0) cc_final: 0.8195 (t70) REVERT: K 118 THR cc_start: 0.9227 (m) cc_final: 0.8921 (p) outliers start: 43 outliers final: 24 residues processed: 366 average time/residue: 0.6491 time to fit residues: 248.7192 Evaluate side-chains 360 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 77 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.068791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.048877 restraints weight = 17889.555| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.70 r_work: 0.3212 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 8096 Z= 0.365 Angle : 0.839 9.490 11000 Z= 0.431 Chirality : 0.054 0.157 1287 Planarity : 0.006 0.050 1353 Dihedral : 5.940 25.956 1089 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.59 % Allowed : 25.87 % Favored : 68.53 % 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 are not related in a simple way. whole: -2.78 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG F 104 TYR 0.023 0.003 TYR A 105 PHE 0.026 0.002 PHE K 64 TRP 0.007 0.001 TRP E 79 HIS 0.005 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00797 ( 8096) covalent geometry : angle 0.83920 (11000) hydrogen bonds : bond 0.03326 ( 192) hydrogen bonds : angle 4.90707 ( 576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8793 (mttt) cc_final: 0.8417 (mtpm) REVERT: A 34 ARG cc_start: 0.8723 (ttt180) cc_final: 0.8147 (tpp80) REVERT: A 62 GLU cc_start: 0.7681 (mp0) cc_final: 0.7351 (mp0) REVERT: A 63 GLU cc_start: 0.8881 (pt0) cc_final: 0.8196 (pp20) REVERT: A 66 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 70 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8826 (tppp) REVERT: A 76 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8654 (mptt) REVERT: A 84 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9170 (pp) REVERT: A 89 GLU cc_start: 0.8265 (pm20) cc_final: 0.8010 (pm20) REVERT: A 104 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7400 (mtm-85) REVERT: A 106 THR cc_start: 0.9195 (m) cc_final: 0.8766 (t) REVERT: B 13 MET cc_start: 0.8213 (tmm) cc_final: 0.7840 (tmm) REVERT: B 18 ASP cc_start: 0.9049 (m-30) cc_final: 0.8773 (m-30) REVERT: B 21 ARG cc_start: 0.8439 (mtp85) cc_final: 0.7985 (tpp80) REVERT: B 30 MET cc_start: 0.8181 (tmm) cc_final: 0.7688 (tmm) REVERT: B 34 ARG cc_start: 0.8812 (ttt180) cc_final: 0.8229 (tpp80) REVERT: B 35 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8894 (mtpp) REVERT: B 62 GLU cc_start: 0.7838 (mp0) cc_final: 0.7126 (mp0) REVERT: B 66 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7420 (tm-30) REVERT: B 80 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8713 (ttpt) REVERT: B 84 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9127 (pp) REVERT: B 90 HIS cc_start: 0.8286 (m90) cc_final: 0.8074 (m90) REVERT: B 99 ASP cc_start: 0.9078 (t70) cc_final: 0.8838 (t70) REVERT: B 104 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7884 (mtm-85) REVERT: C 15 LYS cc_start: 0.8671 (mttt) cc_final: 0.8144 (mtpm) REVERT: C 18 ASP cc_start: 0.8953 (m-30) cc_final: 0.8618 (m-30) REVERT: C 30 MET cc_start: 0.8621 (ttm) cc_final: 0.8038 (tmm) REVERT: C 35 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8893 (ttmt) REVERT: C 62 GLU cc_start: 0.8086 (mp0) cc_final: 0.7625 (mp0) REVERT: C 63 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: C 66 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: C 90 HIS cc_start: 0.8545 (m90) cc_final: 0.8230 (m90) REVERT: D 13 MET cc_start: 0.8165 (tmm) cc_final: 0.7747 (tmm) REVERT: D 15 LYS cc_start: 0.8774 (mttt) cc_final: 0.8222 (mtpm) REVERT: D 34 ARG cc_start: 0.9059 (ttt180) cc_final: 0.8443 (tpp80) REVERT: D 62 GLU cc_start: 0.7945 (mp0) cc_final: 0.7499 (mp0) REVERT: D 63 GLU cc_start: 0.7894 (pm20) cc_final: 0.7593 (pm20) REVERT: D 66 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7877 (tm-30) REVERT: D 70 LYS cc_start: 0.9263 (tttm) cc_final: 0.9041 (ptmm) REVERT: D 80 LYS cc_start: 0.9002 (tttt) cc_final: 0.8659 (tttm) REVERT: D 89 GLU cc_start: 0.8594 (mp0) cc_final: 0.8356 (mp0) REVERT: D 104 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8129 (ttm110) REVERT: D 116 TYR cc_start: 0.9438 (m-80) cc_final: 0.9182 (m-80) REVERT: E 13 MET cc_start: 0.8399 (tmm) cc_final: 0.8064 (tmm) REVERT: E 21 ARG cc_start: 0.8426 (tpt-90) cc_final: 0.8123 (mmm160) REVERT: E 26 ILE cc_start: 0.9213 (mt) cc_final: 0.8945 (mp) REVERT: E 30 MET cc_start: 0.8239 (tmm) cc_final: 0.7553 (tmm) REVERT: E 34 ARG cc_start: 0.9020 (ttt180) cc_final: 0.8421 (tpp80) REVERT: E 35 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8850 (mtpt) REVERT: E 62 GLU cc_start: 0.8526 (pm20) cc_final: 0.7603 (mp0) REVERT: E 66 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 72 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: F 13 MET cc_start: 0.8281 (tmm) cc_final: 0.7520 (tmm) REVERT: F 15 LYS cc_start: 0.8796 (mttt) cc_final: 0.8100 (mttp) REVERT: F 18 ASP cc_start: 0.8930 (m-30) cc_final: 0.8467 (m-30) REVERT: F 30 MET cc_start: 0.8435 (ttm) cc_final: 0.7852 (tmm) REVERT: F 34 ARG cc_start: 0.9003 (ttt180) cc_final: 0.8320 (tpp80) REVERT: F 62 GLU cc_start: 0.8305 (pm20) cc_final: 0.7570 (pm20) REVERT: F 63 GLU cc_start: 0.7948 (pm20) cc_final: 0.7180 (pm20) REVERT: F 80 LYS cc_start: 0.8978 (tttt) cc_final: 0.8662 (tttm) REVERT: G 13 MET cc_start: 0.8670 (tmm) cc_final: 0.7904 (tmm) REVERT: G 15 LYS cc_start: 0.8994 (mttt) cc_final: 0.8344 (mttp) REVERT: G 30 MET cc_start: 0.8293 (tmm) cc_final: 0.7412 (tmm) REVERT: G 34 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8313 (tpp80) REVERT: G 63 GLU cc_start: 0.8567 (pt0) cc_final: 0.7604 (pm20) REVERT: G 66 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7620 (tm-30) REVERT: G 104 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8091 (ttm110) REVERT: H 15 LYS cc_start: 0.8703 (mttt) cc_final: 0.8142 (mtpp) REVERT: H 18 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: H 30 MET cc_start: 0.8598 (mtp) cc_final: 0.8119 (tmm) REVERT: H 34 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8362 (tpp80) REVERT: H 62 GLU cc_start: 0.8317 (mp0) cc_final: 0.7866 (mp0) REVERT: H 63 GLU cc_start: 0.8788 (pt0) cc_final: 0.8066 (pm20) REVERT: H 66 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H 84 ILE cc_start: 0.9397 (mt) cc_final: 0.8925 (pp) REVERT: I 13 MET cc_start: 0.8167 (tmm) cc_final: 0.7850 (tmm) REVERT: I 15 LYS cc_start: 0.8806 (mttt) cc_final: 0.8161 (mtpp) REVERT: I 18 ASP cc_start: 0.8781 (m-30) cc_final: 0.8500 (m-30) REVERT: I 34 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8423 (tpp80) REVERT: I 80 LYS cc_start: 0.8901 (tttt) cc_final: 0.8538 (tttm) REVERT: I 89 GLU cc_start: 0.8206 (pm20) cc_final: 0.7888 (pm20) REVERT: I 99 ASP cc_start: 0.8939 (t0) cc_final: 0.8728 (t0) REVERT: I 100 SER cc_start: 0.8784 (t) cc_final: 0.8496 (p) REVERT: I 104 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7950 (ttm110) REVERT: J 13 MET cc_start: 0.8427 (tmm) cc_final: 0.8125 (tmm) REVERT: J 15 LYS cc_start: 0.8671 (mttt) cc_final: 0.7932 (ttmm) REVERT: J 30 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: J 34 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8277 (ttt-90) REVERT: J 35 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8672 (ttmm) REVERT: J 61 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: J 62 GLU cc_start: 0.8344 (mp0) cc_final: 0.8128 (mp0) REVERT: J 63 GLU cc_start: 0.8665 (pt0) cc_final: 0.8389 (pt0) REVERT: J 66 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7509 (tm-30) REVERT: J 84 ILE cc_start: 0.9336 (mt) cc_final: 0.8824 (pp) REVERT: J 100 SER cc_start: 0.9000 (t) cc_final: 0.8692 (p) REVERT: K 13 MET cc_start: 0.8156 (tmm) cc_final: 0.7932 (tmm) REVERT: K 15 LYS cc_start: 0.8503 (mttt) cc_final: 0.7863 (mtpm) REVERT: K 21 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8351 (mtp85) REVERT: K 26 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8951 (mp) REVERT: K 62 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7875 (mp0) REVERT: K 66 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8191 (tm-30) REVERT: K 80 LYS cc_start: 0.8933 (tttt) cc_final: 0.8537 (tttm) REVERT: K 99 ASP cc_start: 0.8609 (t0) cc_final: 0.8401 (t70) REVERT: K 118 THR cc_start: 0.9179 (m) cc_final: 0.8679 (p) outliers start: 48 outliers final: 27 residues processed: 353 average time/residue: 0.6586 time to fit residues: 242.9848 Evaluate side-chains 363 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 90 HIS K 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.069572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.051043 restraints weight = 17414.054| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.69 r_work: 0.3292 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8096 Z= 0.191 Angle : 0.819 9.820 11000 Z= 0.411 Chirality : 0.052 0.152 1287 Planarity : 0.006 0.061 1353 Dihedral : 5.813 24.548 1089 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.90 % Allowed : 27.86 % Favored : 67.25 % 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 are not related in a simple way. whole: -2.79 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG F 104 TYR 0.021 0.002 TYR K 114 PHE 0.025 0.001 PHE K 64 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8096) covalent geometry : angle 0.81929 (11000) hydrogen bonds : bond 0.02696 ( 192) hydrogen bonds : angle 4.90692 ( 576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 336 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8781 (ttt180) cc_final: 0.8183 (tpp80) REVERT: A 62 GLU cc_start: 0.7707 (mp0) cc_final: 0.7272 (mp0) REVERT: A 63 GLU cc_start: 0.8903 (pt0) cc_final: 0.8129 (pp20) REVERT: A 66 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7633 (tm-30) REVERT: A 70 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8848 (tppp) REVERT: A 90 HIS cc_start: 0.8314 (m90) cc_final: 0.8032 (m90) REVERT: A 92 GLU cc_start: 0.7957 (mp0) cc_final: 0.7651 (mp0) REVERT: A 104 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7346 (mtm-85) REVERT: A 106 THR cc_start: 0.9218 (m) cc_final: 0.8839 (t) REVERT: B 13 MET cc_start: 0.8249 (tmm) cc_final: 0.7721 (tmm) REVERT: B 15 LYS cc_start: 0.8690 (mttt) cc_final: 0.8054 (mtpm) REVERT: B 18 ASP cc_start: 0.9068 (m-30) cc_final: 0.8678 (m-30) REVERT: B 34 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8170 (tpp80) REVERT: B 35 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8884 (mtpp) REVERT: B 62 GLU cc_start: 0.7851 (mp0) cc_final: 0.7019 (mp0) REVERT: B 66 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 80 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8670 (ttpt) REVERT: B 84 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9211 (pp) REVERT: B 104 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: C 15 LYS cc_start: 0.8635 (mttt) cc_final: 0.8141 (mtpm) REVERT: C 18 ASP cc_start: 0.8935 (m-30) cc_final: 0.8573 (m-30) REVERT: C 30 MET cc_start: 0.8549 (ttm) cc_final: 0.8025 (tmm) REVERT: C 35 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8999 (ttmt) REVERT: C 62 GLU cc_start: 0.8054 (mp0) cc_final: 0.7627 (mp0) REVERT: C 63 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: C 66 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: C 84 ILE cc_start: 0.9451 (mm) cc_final: 0.9175 (pp) REVERT: C 90 HIS cc_start: 0.8546 (m90) cc_final: 0.8251 (m90) REVERT: D 13 MET cc_start: 0.8161 (tmm) cc_final: 0.7727 (tmm) REVERT: D 15 LYS cc_start: 0.8708 (mttt) cc_final: 0.8063 (mtpm) REVERT: D 34 ARG cc_start: 0.9048 (ttt180) cc_final: 0.8428 (tpp80) REVERT: D 61 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7834 (mt-10) REVERT: D 62 GLU cc_start: 0.7916 (mp0) cc_final: 0.7563 (mp0) REVERT: D 63 GLU cc_start: 0.7899 (pm20) cc_final: 0.7610 (pm20) REVERT: D 66 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 80 LYS cc_start: 0.8990 (tttt) cc_final: 0.8632 (tttm) REVERT: D 116 TYR cc_start: 0.9452 (m-80) cc_final: 0.9189 (m-80) REVERT: E 13 MET cc_start: 0.8410 (tmm) cc_final: 0.8030 (tmm) REVERT: E 30 MET cc_start: 0.8261 (tmm) cc_final: 0.7575 (tmm) REVERT: E 34 ARG cc_start: 0.9008 (ttt180) cc_final: 0.8371 (tpp80) REVERT: E 35 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8829 (mtpt) REVERT: E 62 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: E 66 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7760 (tm-30) REVERT: E 72 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: F 13 MET cc_start: 0.8276 (tmm) cc_final: 0.7740 (tmm) REVERT: F 15 LYS cc_start: 0.8783 (mttt) cc_final: 0.8326 (mtpp) REVERT: F 18 ASP cc_start: 0.8906 (m-30) cc_final: 0.8559 (m-30) REVERT: F 30 MET cc_start: 0.8363 (ttm) cc_final: 0.7771 (tmm) REVERT: F 34 ARG cc_start: 0.8983 (ttt180) cc_final: 0.8290 (tpp80) REVERT: F 35 LYS cc_start: 0.9286 (ttmt) cc_final: 0.8975 (ttmm) REVERT: F 62 GLU cc_start: 0.8313 (pm20) cc_final: 0.7573 (mp0) REVERT: F 63 GLU cc_start: 0.7934 (pm20) cc_final: 0.7349 (pm20) REVERT: F 80 LYS cc_start: 0.8960 (tttt) cc_final: 0.8645 (tttp) REVERT: F 89 GLU cc_start: 0.7702 (mp0) cc_final: 0.7196 (pm20) REVERT: G 13 MET cc_start: 0.8660 (tmm) cc_final: 0.7948 (tmm) REVERT: G 15 LYS cc_start: 0.8952 (mttt) cc_final: 0.8338 (mttp) REVERT: G 30 MET cc_start: 0.8367 (tmm) cc_final: 0.7425 (tmm) REVERT: G 34 ARG cc_start: 0.8952 (ttt180) cc_final: 0.8350 (tpp80) REVERT: G 61 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: G 63 GLU cc_start: 0.8534 (pt0) cc_final: 0.7589 (pm20) REVERT: G 66 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7430 (tm-30) REVERT: H 15 LYS cc_start: 0.8712 (mttt) cc_final: 0.8135 (mtpp) REVERT: H 30 MET cc_start: 0.8518 (mtp) cc_final: 0.8143 (tmm) REVERT: H 34 ARG cc_start: 0.8975 (ttt180) cc_final: 0.8331 (tpp80) REVERT: H 62 GLU cc_start: 0.8285 (mp0) cc_final: 0.7850 (mp0) REVERT: H 63 GLU cc_start: 0.8730 (pt0) cc_final: 0.8013 (pm20) REVERT: H 66 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 84 ILE cc_start: 0.9361 (mt) cc_final: 0.8872 (pp) REVERT: I 13 MET cc_start: 0.8156 (tmm) cc_final: 0.7752 (tmm) REVERT: I 15 LYS cc_start: 0.8685 (mttt) cc_final: 0.8013 (mtpp) REVERT: I 18 ASP cc_start: 0.8774 (m-30) cc_final: 0.8451 (m-30) REVERT: I 34 ARG cc_start: 0.8807 (ttt180) cc_final: 0.8432 (tpp80) REVERT: I 72 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8424 (mp0) REVERT: I 80 LYS cc_start: 0.8882 (tttt) cc_final: 0.8526 (tttp) REVERT: I 89 GLU cc_start: 0.8193 (pm20) cc_final: 0.7701 (mp0) REVERT: I 99 ASP cc_start: 0.8875 (t0) cc_final: 0.8310 (t70) REVERT: I 100 SER cc_start: 0.8785 (t) cc_final: 0.8501 (p) REVERT: I 104 ARG cc_start: 0.8251 (mtm-85) cc_final: 0.7841 (ttm110) REVERT: J 13 MET cc_start: 0.8479 (tmm) cc_final: 0.8145 (tmm) REVERT: J 15 LYS cc_start: 0.8633 (mttt) cc_final: 0.7907 (ttmm) REVERT: J 21 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8013 (mmm-85) REVERT: J 30 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7919 (tmm) REVERT: J 34 ARG cc_start: 0.8646 (ttt180) cc_final: 0.8256 (ttt-90) REVERT: J 35 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8760 (ttmm) REVERT: J 61 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: J 63 GLU cc_start: 0.8671 (pt0) cc_final: 0.8456 (pt0) REVERT: J 66 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7596 (tm-30) REVERT: J 84 ILE cc_start: 0.9358 (mt) cc_final: 0.8839 (pp) REVERT: J 100 SER cc_start: 0.8942 (t) cc_final: 0.8555 (p) REVERT: K 13 MET cc_start: 0.8138 (tmm) cc_final: 0.7885 (tmm) REVERT: K 15 LYS cc_start: 0.8464 (mttt) cc_final: 0.7875 (mtpm) REVERT: K 21 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8373 (mtp85) REVERT: K 26 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8916 (mp) REVERT: K 62 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7807 (mp0) REVERT: K 66 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8228 (tm-30) REVERT: K 80 LYS cc_start: 0.8899 (tttt) cc_final: 0.8517 (tttm) REVERT: K 99 ASP cc_start: 0.8526 (t0) cc_final: 0.8221 (t70) REVERT: K 118 THR cc_start: 0.9170 (m) cc_final: 0.8671 (p) outliers start: 42 outliers final: 21 residues processed: 355 average time/residue: 0.6751 time to fit residues: 250.6130 Evaluate side-chains 357 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 68 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.0020 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.068280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.048925 restraints weight = 17930.552| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.68 r_work: 0.3131 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 8096 Z= 0.395 Angle : 0.912 10.008 11000 Z= 0.467 Chirality : 0.055 0.287 1287 Planarity : 0.007 0.065 1353 Dihedral : 6.014 25.308 1089 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.66 % Allowed : 29.72 % Favored : 65.62 % 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 are not related in a simple way. whole: -2.87 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG F 104 TYR 0.028 0.003 TYR I 116 PHE 0.026 0.002 PHE K 64 TRP 0.008 0.002 TRP E 79 HIS 0.007 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00857 ( 8096) covalent geometry : angle 0.91238 (11000) hydrogen bonds : bond 0.03354 ( 192) hydrogen bonds : angle 4.86816 ( 576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8865 (mttt) cc_final: 0.8473 (mtpm) REVERT: A 34 ARG cc_start: 0.8726 (ttt180) cc_final: 0.8154 (tpp80) REVERT: A 62 GLU cc_start: 0.7739 (mp0) cc_final: 0.7401 (mp0) REVERT: A 63 GLU cc_start: 0.8916 (pt0) cc_final: 0.8196 (pp20) REVERT: A 66 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 70 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8815 (tppp) REVERT: A 90 HIS cc_start: 0.8366 (m90) cc_final: 0.8109 (m90) REVERT: A 104 ARG cc_start: 0.8138 (mtm-85) cc_final: 0.7461 (mtm-85) REVERT: A 106 THR cc_start: 0.9159 (m) cc_final: 0.8721 (t) REVERT: B 13 MET cc_start: 0.8289 (tmm) cc_final: 0.7939 (tmm) REVERT: B 18 ASP cc_start: 0.9070 (m-30) cc_final: 0.8785 (m-30) REVERT: B 21 ARG cc_start: 0.8486 (mtp85) cc_final: 0.8031 (tpp80) REVERT: B 34 ARG cc_start: 0.8838 (ttt180) cc_final: 0.8276 (tpp80) REVERT: B 35 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8878 (mtpp) REVERT: B 62 GLU cc_start: 0.7883 (mp0) cc_final: 0.7158 (mp0) REVERT: B 66 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7688 (tm-30) REVERT: B 80 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8661 (ttpt) REVERT: B 104 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7712 (mtm-85) REVERT: C 15 LYS cc_start: 0.8704 (mttt) cc_final: 0.8146 (mtpm) REVERT: C 18 ASP cc_start: 0.9010 (m-30) cc_final: 0.8661 (m-30) REVERT: C 30 MET cc_start: 0.8727 (ttm) cc_final: 0.8057 (tmm) REVERT: C 35 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8938 (ttmt) REVERT: C 62 GLU cc_start: 0.8135 (mp0) cc_final: 0.7806 (mp0) REVERT: C 63 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: C 90 HIS cc_start: 0.8546 (m90) cc_final: 0.8177 (m90) REVERT: D 13 MET cc_start: 0.8241 (tmm) cc_final: 0.7790 (tmm) REVERT: D 15 LYS cc_start: 0.8783 (mttt) cc_final: 0.8177 (mtpm) REVERT: D 34 ARG cc_start: 0.9074 (ttt180) cc_final: 0.8456 (tpp80) REVERT: D 62 GLU cc_start: 0.7934 (mp0) cc_final: 0.7552 (mp0) REVERT: D 63 GLU cc_start: 0.7931 (pm20) cc_final: 0.7609 (pm20) REVERT: D 66 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 80 LYS cc_start: 0.8986 (tttt) cc_final: 0.8629 (tttm) REVERT: D 89 GLU cc_start: 0.8455 (mp0) cc_final: 0.8224 (mp0) REVERT: D 104 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8218 (ttm110) REVERT: E 13 MET cc_start: 0.8402 (tmm) cc_final: 0.8032 (tmm) REVERT: E 26 ILE cc_start: 0.9224 (mt) cc_final: 0.8958 (mp) REVERT: E 30 MET cc_start: 0.8451 (tmm) cc_final: 0.7647 (tmm) REVERT: E 34 ARG cc_start: 0.9040 (ttt180) cc_final: 0.8401 (tpp80) REVERT: E 35 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8867 (mtpt) REVERT: E 62 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: E 66 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7642 (tm-30) REVERT: E 72 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8437 (mp0) REVERT: F 13 MET cc_start: 0.8326 (tmm) cc_final: 0.7839 (tmm) REVERT: F 15 LYS cc_start: 0.8822 (mttt) cc_final: 0.8449 (mtpp) REVERT: F 18 ASP cc_start: 0.8932 (m-30) cc_final: 0.8582 (m-30) REVERT: F 30 MET cc_start: 0.8513 (ttm) cc_final: 0.7891 (tmm) REVERT: F 34 ARG cc_start: 0.8993 (ttt180) cc_final: 0.8348 (tpp80) REVERT: F 35 LYS cc_start: 0.9328 (ttmt) cc_final: 0.8967 (ttmm) REVERT: F 62 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: F 63 GLU cc_start: 0.7980 (pm20) cc_final: 0.7228 (pm20) REVERT: F 80 LYS cc_start: 0.8997 (tttt) cc_final: 0.8684 (tttm) REVERT: F 89 GLU cc_start: 0.7763 (mp0) cc_final: 0.7294 (pm20) REVERT: G 13 MET cc_start: 0.8669 (tmm) cc_final: 0.8291 (tmm) REVERT: G 30 MET cc_start: 0.8560 (tmm) cc_final: 0.7576 (tmm) REVERT: G 34 ARG cc_start: 0.8964 (ttt180) cc_final: 0.8335 (tpp80) REVERT: G 63 GLU cc_start: 0.8598 (pt0) cc_final: 0.7614 (pm20) REVERT: G 66 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7570 (tm-30) REVERT: G 89 GLU cc_start: 0.8377 (mp0) cc_final: 0.8025 (mp0) REVERT: H 15 LYS cc_start: 0.8686 (mttt) cc_final: 0.8136 (mtpp) REVERT: H 30 MET cc_start: 0.8719 (mtp) cc_final: 0.8164 (tmm) REVERT: H 34 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8345 (tpp80) REVERT: H 62 GLU cc_start: 0.8381 (mp0) cc_final: 0.7858 (mp0) REVERT: H 63 GLU cc_start: 0.8828 (pt0) cc_final: 0.8105 (pm20) REVERT: H 66 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7844 (tm-30) REVERT: H 84 ILE cc_start: 0.9419 (mt) cc_final: 0.8930 (pp) REVERT: I 13 MET cc_start: 0.8278 (tmm) cc_final: 0.7884 (tmm) REVERT: I 15 LYS cc_start: 0.8812 (mttt) cc_final: 0.8176 (mtpp) REVERT: I 18 ASP cc_start: 0.8778 (m-30) cc_final: 0.8442 (m-30) REVERT: I 34 ARG cc_start: 0.8789 (ttt180) cc_final: 0.8422 (tpp80) REVERT: I 72 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8459 (mp0) REVERT: I 80 LYS cc_start: 0.8919 (tttt) cc_final: 0.8527 (tttm) REVERT: I 99 ASP cc_start: 0.8992 (t0) cc_final: 0.8765 (t0) REVERT: I 100 SER cc_start: 0.8793 (t) cc_final: 0.8526 (p) REVERT: I 104 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7895 (ttm110) REVERT: J 13 MET cc_start: 0.8427 (tmm) cc_final: 0.7445 (tmm) REVERT: J 15 LYS cc_start: 0.8671 (mttt) cc_final: 0.7803 (mtmm) REVERT: J 21 ARG cc_start: 0.8403 (mmm160) cc_final: 0.8087 (mmm-85) REVERT: J 30 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8126 (mmm) REVERT: J 34 ARG cc_start: 0.8669 (ttt180) cc_final: 0.8286 (ttt-90) REVERT: J 35 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8669 (ttmm) REVERT: J 62 GLU cc_start: 0.8366 (mp0) cc_final: 0.8165 (mp0) REVERT: J 63 GLU cc_start: 0.8815 (pt0) cc_final: 0.8494 (pt0) REVERT: J 66 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7801 (tm-30) REVERT: J 84 ILE cc_start: 0.9373 (mt) cc_final: 0.8863 (pp) REVERT: J 100 SER cc_start: 0.9033 (t) cc_final: 0.8725 (p) REVERT: K 13 MET cc_start: 0.8173 (tmm) cc_final: 0.7943 (tmm) REVERT: K 15 LYS cc_start: 0.8485 (mttt) cc_final: 0.7930 (mtpm) REVERT: K 21 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8336 (mtp85) REVERT: K 62 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7869 (mp0) REVERT: K 66 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8266 (tm-30) REVERT: K 73 ILE cc_start: 0.8369 (mt) cc_final: 0.7993 (mp) REVERT: K 80 LYS cc_start: 0.8921 (tttt) cc_final: 0.8502 (tttm) REVERT: K 99 ASP cc_start: 0.8683 (t0) cc_final: 0.8469 (t70) outliers start: 40 outliers final: 24 residues processed: 347 average time/residue: 0.7161 time to fit residues: 259.4174 Evaluate side-chains 353 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.072752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.053558 restraints weight = 16954.533| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.68 r_work: 0.3337 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8096 Z= 0.164 Angle : 0.875 10.067 11000 Z= 0.438 Chirality : 0.052 0.153 1287 Planarity : 0.006 0.077 1353 Dihedral : 5.797 23.328 1089 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.38 % Allowed : 31.70 % Favored : 64.92 % 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 are not related in a simple way. whole: -2.90 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG F 104 TYR 0.020 0.002 TYR E 105 PHE 0.029 0.001 PHE K 64 TRP 0.002 0.001 TRP G 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8096) covalent geometry : angle 0.87495 (11000) hydrogen bonds : bond 0.02440 ( 192) hydrogen bonds : angle 4.85257 ( 576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8836 (ttt180) cc_final: 0.8227 (tpp80) REVERT: A 61 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 62 GLU cc_start: 0.7756 (mp0) cc_final: 0.7400 (mp0) REVERT: A 63 GLU cc_start: 0.8904 (pt0) cc_final: 0.7925 (pp20) REVERT: A 66 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 70 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8821 (tppp) REVERT: A 90 HIS cc_start: 0.8568 (m90) cc_final: 0.8189 (m90) REVERT: A 104 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7397 (mtm-85) REVERT: A 106 THR cc_start: 0.9250 (m) cc_final: 0.8922 (t) REVERT: B 13 MET cc_start: 0.8266 (tmm) cc_final: 0.7941 (tmm) REVERT: B 18 ASP cc_start: 0.9057 (m-30) cc_final: 0.8754 (m-30) REVERT: B 34 ARG cc_start: 0.8796 (ttt180) cc_final: 0.8270 (tpp80) REVERT: B 61 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7975 (mt-10) REVERT: B 62 GLU cc_start: 0.7919 (mp0) cc_final: 0.7076 (mp0) REVERT: B 63 GLU cc_start: 0.7826 (pm20) cc_final: 0.7398 (pm20) REVERT: B 66 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 69 TYR cc_start: 0.9369 (m-80) cc_final: 0.9166 (m-80) REVERT: B 80 LYS cc_start: 0.9007 (ttpt) cc_final: 0.8614 (ttpt) REVERT: C 15 LYS cc_start: 0.8665 (mttt) cc_final: 0.8136 (mtpm) REVERT: C 18 ASP cc_start: 0.8946 (m-30) cc_final: 0.8565 (m-30) REVERT: C 30 MET cc_start: 0.8622 (ttm) cc_final: 0.8135 (tmm) REVERT: C 35 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8716 (mttt) REVERT: C 62 GLU cc_start: 0.8055 (mp0) cc_final: 0.7774 (mp0) REVERT: C 63 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: C 69 TYR cc_start: 0.9347 (m-80) cc_final: 0.9141 (m-80) REVERT: C 90 HIS cc_start: 0.8538 (m90) cc_final: 0.8289 (m90) REVERT: D 13 MET cc_start: 0.8170 (tmm) cc_final: 0.7697 (tmm) REVERT: D 15 LYS cc_start: 0.8707 (mttt) cc_final: 0.8088 (mtpm) REVERT: D 34 ARG cc_start: 0.9069 (ttt180) cc_final: 0.8453 (tpp80) REVERT: D 61 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 62 GLU cc_start: 0.7885 (mp0) cc_final: 0.7524 (mp0) REVERT: D 63 GLU cc_start: 0.7901 (pm20) cc_final: 0.7574 (pm20) REVERT: D 66 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7618 (tm-30) REVERT: D 72 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8529 (mm-30) REVERT: D 80 LYS cc_start: 0.8975 (tttt) cc_final: 0.8605 (tttp) REVERT: D 104 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.8031 (ttm110) REVERT: D 116 TYR cc_start: 0.9412 (m-80) cc_final: 0.9206 (m-80) REVERT: E 13 MET cc_start: 0.8424 (tmm) cc_final: 0.8066 (tmm) REVERT: E 30 MET cc_start: 0.8446 (tmm) cc_final: 0.7697 (tmm) REVERT: E 34 ARG cc_start: 0.9053 (ttt180) cc_final: 0.8444 (tpp80) REVERT: E 35 LYS cc_start: 0.9068 (ttmt) cc_final: 0.8836 (mtpt) REVERT: E 62 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: E 66 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 72 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8378 (mp0) REVERT: E 89 GLU cc_start: 0.8427 (mp0) cc_final: 0.8154 (mp0) REVERT: F 13 MET cc_start: 0.8259 (tmm) cc_final: 0.7683 (tmm) REVERT: F 15 LYS cc_start: 0.8751 (mttt) cc_final: 0.7997 (mtpm) REVERT: F 18 ASP cc_start: 0.8922 (m-30) cc_final: 0.8539 (m-30) REVERT: F 30 MET cc_start: 0.8385 (ttm) cc_final: 0.7888 (tmm) REVERT: F 34 ARG cc_start: 0.9016 (ttt180) cc_final: 0.8311 (tpp80) REVERT: F 35 LYS cc_start: 0.9286 (ttmt) cc_final: 0.8950 (ttmm) REVERT: F 62 GLU cc_start: 0.8341 (pm20) cc_final: 0.7603 (pm20) REVERT: F 63 GLU cc_start: 0.7928 (pm20) cc_final: 0.7113 (pm20) REVERT: F 80 LYS cc_start: 0.8972 (tttt) cc_final: 0.8660 (tttm) REVERT: F 89 GLU cc_start: 0.7768 (mp0) cc_final: 0.7235 (pm20) REVERT: F 106 THR cc_start: 0.9115 (m) cc_final: 0.8893 (t) REVERT: G 13 MET cc_start: 0.8644 (tmm) cc_final: 0.7956 (tmm) REVERT: G 15 LYS cc_start: 0.8947 (mttt) cc_final: 0.8311 (mttp) REVERT: G 30 MET cc_start: 0.8553 (tmm) cc_final: 0.7686 (tmm) REVERT: G 34 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8356 (tpp80) REVERT: G 63 GLU cc_start: 0.8525 (pt0) cc_final: 0.7474 (pm20) REVERT: G 66 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 89 GLU cc_start: 0.8353 (mp0) cc_final: 0.8001 (mp0) REVERT: H 15 LYS cc_start: 0.8676 (mttt) cc_final: 0.8163 (mtpp) REVERT: H 30 MET cc_start: 0.8557 (mtp) cc_final: 0.8141 (tmm) REVERT: H 34 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8415 (tpp80) REVERT: H 35 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8581 (mttt) REVERT: H 62 GLU cc_start: 0.8421 (mp0) cc_final: 0.7806 (mp0) REVERT: H 63 GLU cc_start: 0.8772 (pt0) cc_final: 0.8084 (pm20) REVERT: H 66 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7584 (tm-30) REVERT: H 84 ILE cc_start: 0.9409 (mt) cc_final: 0.8940 (pp) REVERT: I 13 MET cc_start: 0.8174 (tmm) cc_final: 0.7929 (tmm) REVERT: I 18 ASP cc_start: 0.8814 (m-30) cc_final: 0.8315 (m-30) REVERT: I 34 ARG cc_start: 0.8812 (ttt180) cc_final: 0.8439 (tpp80) REVERT: I 35 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8920 (mtpp) REVERT: I 72 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8554 (mp0) REVERT: I 80 LYS cc_start: 0.8885 (tttt) cc_final: 0.8508 (tttm) REVERT: I 89 GLU cc_start: 0.8529 (pm20) cc_final: 0.8120 (mp0) REVERT: I 99 ASP cc_start: 0.8886 (t0) cc_final: 0.8321 (t70) REVERT: I 100 SER cc_start: 0.8791 (t) cc_final: 0.8509 (p) REVERT: I 104 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7797 (ttm110) REVERT: J 13 MET cc_start: 0.8444 (tmm) cc_final: 0.8097 (tmm) REVERT: J 18 ASP cc_start: 0.8730 (m-30) cc_final: 0.8458 (m-30) REVERT: J 21 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8078 (mmm-85) REVERT: J 30 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8142 (mmm) REVERT: J 34 ARG cc_start: 0.8680 (ttt180) cc_final: 0.8293 (ttt-90) REVERT: J 35 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8705 (ttmm) REVERT: J 62 GLU cc_start: 0.8331 (mp0) cc_final: 0.8090 (mp0) REVERT: J 63 GLU cc_start: 0.8770 (pt0) cc_final: 0.8549 (pt0) REVERT: J 66 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7634 (tm-30) REVERT: J 72 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8254 (mp0) REVERT: J 84 ILE cc_start: 0.9382 (mt) cc_final: 0.8895 (pp) REVERT: J 89 GLU cc_start: 0.8132 (mp0) cc_final: 0.7579 (mp0) REVERT: J 100 SER cc_start: 0.8926 (t) cc_final: 0.8562 (p) REVERT: K 13 MET cc_start: 0.8204 (tmm) cc_final: 0.7995 (tmm) REVERT: K 15 LYS cc_start: 0.8557 (mttt) cc_final: 0.7920 (mtpm) REVERT: K 21 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.8314 (mtp85) REVERT: K 62 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7850 (mp0) REVERT: K 66 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8134 (tm-30) REVERT: K 80 LYS cc_start: 0.8894 (tttt) cc_final: 0.8505 (tttm) REVERT: K 89 GLU cc_start: 0.9034 (mp0) cc_final: 0.8820 (mp0) REVERT: K 99 ASP cc_start: 0.8409 (t0) cc_final: 0.8159 (t70) outliers start: 29 outliers final: 12 residues processed: 361 average time/residue: 0.6659 time to fit residues: 251.8304 Evaluate side-chains 341 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 325 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.070756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.052823 restraints weight = 17381.804| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.57 r_work: 0.3335 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8096 Z= 0.264 Angle : 0.919 12.100 11000 Z= 0.459 Chirality : 0.054 0.229 1287 Planarity : 0.007 0.087 1353 Dihedral : 5.832 25.772 1089 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.56 % Allowed : 31.82 % Favored : 65.62 % 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 are not related in a simple way. whole: -2.88 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG F 104 TYR 0.020 0.003 TYR E 116 PHE 0.023 0.002 PHE K 64 TRP 0.004 0.001 TRP E 79 HIS 0.004 0.001 HIS I 88 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 8096) covalent geometry : angle 0.91907 (11000) hydrogen bonds : bond 0.02777 ( 192) hydrogen bonds : angle 4.80434 ( 576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 326 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8775 (ttt180) cc_final: 0.8193 (tpp80) REVERT: A 62 GLU cc_start: 0.7756 (mp0) cc_final: 0.7264 (mp0) REVERT: A 63 GLU cc_start: 0.8885 (pt0) cc_final: 0.8124 (pp20) REVERT: A 66 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 70 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8839 (tppp) REVERT: A 90 HIS cc_start: 0.8513 (m90) cc_final: 0.8209 (m90) REVERT: A 104 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: A 106 THR cc_start: 0.9219 (m) cc_final: 0.8844 (t) REVERT: B 13 MET cc_start: 0.8284 (tmm) cc_final: 0.7945 (tmm) REVERT: B 18 ASP cc_start: 0.9094 (m-30) cc_final: 0.8790 (m-30) REVERT: B 34 ARG cc_start: 0.8816 (ttt180) cc_final: 0.8238 (tpp80) REVERT: B 61 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 62 GLU cc_start: 0.7894 (mp0) cc_final: 0.7164 (mp0) REVERT: B 66 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 80 LYS cc_start: 0.9003 (ttpt) cc_final: 0.8630 (ttpt) REVERT: B 104 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7609 (mtm-85) REVERT: C 15 LYS cc_start: 0.8683 (mttt) cc_final: 0.8143 (mtpm) REVERT: C 18 ASP cc_start: 0.8983 (m-30) cc_final: 0.8548 (m-30) REVERT: C 30 MET cc_start: 0.8691 (ttm) cc_final: 0.8047 (tmm) REVERT: C 62 GLU cc_start: 0.8093 (mp0) cc_final: 0.7653 (mp0) REVERT: C 63 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: C 90 HIS cc_start: 0.8522 (m90) cc_final: 0.8311 (m90) REVERT: D 13 MET cc_start: 0.8131 (tmm) cc_final: 0.7680 (tmm) REVERT: D 15 LYS cc_start: 0.8733 (mttt) cc_final: 0.8117 (mtpm) REVERT: D 34 ARG cc_start: 0.9065 (ttt180) cc_final: 0.8443 (tpp80) REVERT: D 62 GLU cc_start: 0.7924 (mp0) cc_final: 0.7547 (mp0) REVERT: D 66 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 80 LYS cc_start: 0.8974 (tttt) cc_final: 0.8615 (tttm) REVERT: D 104 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8094 (ttm110) REVERT: E 13 MET cc_start: 0.8373 (tmm) cc_final: 0.8012 (tmm) REVERT: E 30 MET cc_start: 0.8381 (tmm) cc_final: 0.7702 (tmm) REVERT: E 34 ARG cc_start: 0.9025 (ttt180) cc_final: 0.8390 (tpp80) REVERT: E 35 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8857 (mtpt) REVERT: E 62 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: E 66 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7714 (tm-30) REVERT: E 72 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8389 (mp0) REVERT: F 13 MET cc_start: 0.8250 (tmm) cc_final: 0.7689 (tmm) REVERT: F 15 LYS cc_start: 0.8712 (mttt) cc_final: 0.7988 (mtpm) REVERT: F 18 ASP cc_start: 0.8935 (m-30) cc_final: 0.8548 (m-30) REVERT: F 30 MET cc_start: 0.8512 (ttm) cc_final: 0.7886 (tmm) REVERT: F 34 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8215 (tpp80) REVERT: F 35 LYS cc_start: 0.9282 (ttmt) cc_final: 0.8874 (ttmm) REVERT: F 62 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: F 63 GLU cc_start: 0.7981 (pm20) cc_final: 0.7153 (pm20) REVERT: F 80 LYS cc_start: 0.8971 (tttt) cc_final: 0.8666 (tttp) REVERT: F 89 GLU cc_start: 0.7792 (mp0) cc_final: 0.7373 (pm20) REVERT: G 13 MET cc_start: 0.8630 (tmm) cc_final: 0.7900 (tmm) REVERT: G 15 LYS cc_start: 0.8922 (mttt) cc_final: 0.8301 (mttp) REVERT: G 30 MET cc_start: 0.8558 (tmm) cc_final: 0.7649 (tmm) REVERT: G 34 ARG cc_start: 0.8950 (ttt180) cc_final: 0.8306 (tpp80) REVERT: G 63 GLU cc_start: 0.8558 (pt0) cc_final: 0.7498 (pm20) REVERT: G 66 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7766 (tm-30) REVERT: H 15 LYS cc_start: 0.8687 (mttt) cc_final: 0.8172 (mtpp) REVERT: H 30 MET cc_start: 0.8606 (mtp) cc_final: 0.8128 (tmm) REVERT: H 34 ARG cc_start: 0.8942 (ttt180) cc_final: 0.8333 (tpp80) REVERT: H 35 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8572 (mttt) REVERT: H 62 GLU cc_start: 0.8357 (mp0) cc_final: 0.7846 (mp0) REVERT: H 63 GLU cc_start: 0.8767 (pt0) cc_final: 0.8092 (pm20) REVERT: H 66 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7696 (tm-30) REVERT: H 84 ILE cc_start: 0.9400 (mt) cc_final: 0.8912 (pp) REVERT: I 13 MET cc_start: 0.8228 (tmm) cc_final: 0.7865 (tmm) REVERT: I 18 ASP cc_start: 0.8824 (m-30) cc_final: 0.8296 (m-30) REVERT: I 34 ARG cc_start: 0.8832 (ttt180) cc_final: 0.8385 (tpp80) REVERT: I 35 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8898 (mtpp) REVERT: I 80 LYS cc_start: 0.8895 (tttt) cc_final: 0.8499 (tttp) REVERT: I 89 GLU cc_start: 0.8429 (pm20) cc_final: 0.7559 (pm20) REVERT: I 99 ASP cc_start: 0.8945 (t0) cc_final: 0.8457 (t70) REVERT: I 100 SER cc_start: 0.8810 (t) cc_final: 0.8542 (p) REVERT: I 104 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.7822 (ttm110) REVERT: J 13 MET cc_start: 0.8418 (tmm) cc_final: 0.7973 (tmm) REVERT: J 15 LYS cc_start: 0.8649 (mttt) cc_final: 0.7968 (mtpp) REVERT: J 18 ASP cc_start: 0.8686 (m-30) cc_final: 0.8472 (m-30) REVERT: J 21 ARG cc_start: 0.8387 (mmm160) cc_final: 0.8080 (mmm-85) REVERT: J 30 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8104 (mmm) REVERT: J 34 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8297 (ttt-90) REVERT: J 35 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8691 (ttmm) REVERT: J 61 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7859 (mt-10) REVERT: J 62 GLU cc_start: 0.8330 (mp0) cc_final: 0.8069 (mp0) REVERT: J 63 GLU cc_start: 0.8776 (pt0) cc_final: 0.8559 (pt0) REVERT: J 66 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7654 (tm-30) REVERT: J 72 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8302 (mp0) REVERT: J 84 ILE cc_start: 0.9361 (mt) cc_final: 0.8826 (pp) REVERT: J 100 SER cc_start: 0.8958 (t) cc_final: 0.8620 (p) REVERT: K 13 MET cc_start: 0.8099 (tmm) cc_final: 0.7896 (tmm) REVERT: K 15 LYS cc_start: 0.8491 (mttt) cc_final: 0.7998 (mtpm) REVERT: K 21 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8345 (mtp85) REVERT: K 62 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7867 (mp0) REVERT: K 66 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8086 (tm-30) REVERT: K 80 LYS cc_start: 0.8892 (tttt) cc_final: 0.8501 (tttm) outliers start: 22 outliers final: 15 residues processed: 337 average time/residue: 0.7325 time to fit residues: 257.6708 Evaluate side-chains 338 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 318 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 70 LYS Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS H 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.070846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.052798 restraints weight = 17442.034| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.53 r_work: 0.3326 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8096 Z= 0.268 Angle : 0.928 11.606 11000 Z= 0.467 Chirality : 0.053 0.176 1287 Planarity : 0.007 0.083 1353 Dihedral : 5.908 25.687 1089 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.56 % Allowed : 32.63 % Favored : 64.80 % 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 are not related in a simple way. whole: -2.90 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG F 104 TYR 0.027 0.003 TYR E 116 PHE 0.026 0.002 PHE K 64 TRP 0.005 0.001 TRP E 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 8096) covalent geometry : angle 0.92784 (11000) hydrogen bonds : bond 0.02815 ( 192) hydrogen bonds : angle 4.80989 ( 576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.62 seconds wall clock time: 69 minutes 19.71 seconds (4159.71 seconds total)