Starting phenix.real_space_refine on Wed Mar 12 10:25:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_10150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_10150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_10150.map" model { file = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_10150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sdz_10150/03_2025/6sdz_10150.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.34, per 1000 atoms: 0.93 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: 3.26 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.94 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: 4.04 Time building geometry restraints manager: 3.57 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: 0.01 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: 104.370 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 32.910 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:71.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 210.090 ------------------------------------------------------------------------------- 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= 0.601 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 : 27.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (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 TRP 0.014 0.005 TRP E 79 HIS 0.037 0.004 HIS G 31 PHE 0.075 0.006 PHE K 64 TYR 0.091 0.009 TYR A 114 ARG 0.010 0.001 ARG A 34 *********************** 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 : 1.420 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: 0.8659 (mttt) cc_final: 0.8115 (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: 1.5792 time to fit residues: 652.5760 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 : 0.882 ------------------------------------------------------------------------------- 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 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.074980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.056227 restraints weight = 16731.324| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.65 r_work: 0.3409 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8096 Z= 0.249 Angle : 0.789 8.875 11000 Z= 0.408 Chirality : 0.054 0.145 1287 Planarity : 0.005 0.044 1353 Dihedral : 5.994 25.096 1091 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.20 % Allowed : 20.51 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.22), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.006 0.002 HIS B 88 PHE 0.019 0.001 PHE K 64 TYR 0.026 0.002 TYR K 114 ARG 0.012 0.002 ARG K 104 *********************** 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 405 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8506 (tmm) cc_final: 0.8256 (tmm) REVERT: A 15 LYS cc_start: 0.8915 (mttt) cc_final: 0.8247 (mtpm) REVERT: A 18 ASP cc_start: 0.8526 (m-30) cc_final: 0.8293 (m-30) REVERT: A 34 ARG cc_start: 0.8680 (ttt180) cc_final: 0.7953 (tpp80) REVERT: A 63 GLU cc_start: 0.8871 (pt0) cc_final: 0.8228 (pp20) REVERT: A 66 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 88 HIS cc_start: 0.9257 (t-90) cc_final: 0.8987 (t-90) REVERT: A 89 GLU cc_start: 0.7488 (mp0) cc_final: 0.7148 (pm20) REVERT: A 90 HIS cc_start: 0.8329 (m90) cc_final: 0.8053 (m90) REVERT: A 104 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7904 (mtt-85) REVERT: A 106 THR cc_start: 0.9261 (m) cc_final: 0.8932 (p) REVERT: B 13 MET cc_start: 0.7950 (tmm) cc_final: 0.7562 (tmm) REVERT: B 15 LYS cc_start: 0.8657 (mttt) cc_final: 0.8170 (mtpp) REVERT: B 21 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7892 (tpp80) REVERT: B 34 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8079 (tpp80) REVERT: B 62 GLU cc_start: 0.7983 (mp0) cc_final: 0.7665 (mp0) REVERT: B 66 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 80 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8628 (ttpt) REVERT: B 90 HIS cc_start: 0.8200 (m90) cc_final: 0.7815 (m90) REVERT: B 92 GLU cc_start: 0.7061 (mp0) cc_final: 0.6748 (mp0) REVERT: B 99 ASP cc_start: 0.9013 (t70) cc_final: 0.8791 (t70) REVERT: B 104 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7945 (ttm110) REVERT: C 30 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: C 63 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: C 66 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 90 HIS cc_start: 0.8319 (m90) cc_final: 0.8071 (m90) REVERT: D 13 MET cc_start: 0.7988 (tmm) cc_final: 0.7266 (tmm) REVERT: D 15 LYS cc_start: 0.8417 (mttt) cc_final: 0.7773 (mtpm) REVERT: D 21 ARG cc_start: 0.8484 (mmm160) cc_final: 0.8225 (mmm160) REVERT: D 34 ARG cc_start: 0.8952 (ttt180) cc_final: 0.8416 (tpp80) REVERT: D 63 GLU cc_start: 0.7872 (pm20) cc_final: 0.7612 (pm20) REVERT: D 66 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 69 TYR cc_start: 0.8483 (m-80) cc_final: 0.8087 (m-80) REVERT: D 80 LYS cc_start: 0.8885 (tttt) cc_final: 0.8560 (tttp) REVERT: D 99 ASP cc_start: 0.8962 (t70) cc_final: 0.8742 (t70) REVERT: D 104 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8368 (mtm-85) REVERT: D 116 TYR cc_start: 0.9455 (m-80) cc_final: 0.9119 (m-80) REVERT: E 13 MET cc_start: 0.8194 (tmm) cc_final: 0.7348 (tmm) REVERT: E 15 LYS cc_start: 0.8754 (mttt) cc_final: 0.8188 (mttm) REVERT: E 21 ARG cc_start: 0.8404 (tpt-90) cc_final: 0.8082 (tpp80) REVERT: E 26 ILE cc_start: 0.9118 (mt) cc_final: 0.8862 (mp) REVERT: E 30 MET cc_start: 0.7389 (tmm) cc_final: 0.7021 (tmm) REVERT: E 34 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8352 (tpp80) REVERT: E 62 GLU cc_start: 0.8116 (pm20) cc_final: 0.7911 (pm20) REVERT: E 66 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7698 (tm-30) REVERT: E 69 TYR cc_start: 0.9210 (m-80) cc_final: 0.8889 (m-80) REVERT: E 104 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8036 (mtm-85) REVERT: E 116 TYR cc_start: 0.9339 (m-80) cc_final: 0.9043 (m-80) REVERT: F 13 MET cc_start: 0.7766 (tmm) cc_final: 0.7048 (tmm) REVERT: F 15 LYS cc_start: 0.8538 (mttt) cc_final: 0.7956 (mtpm) REVERT: F 21 ARG cc_start: 0.8567 (tpt-90) cc_final: 0.8160 (mmm160) REVERT: F 30 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7923 (tmm) REVERT: F 34 ARG cc_start: 0.8935 (ttt180) cc_final: 0.8427 (tpp80) REVERT: F 63 GLU cc_start: 0.7873 (pm20) cc_final: 0.7098 (pm20) REVERT: F 66 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 72 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8582 (mt-10) REVERT: F 80 LYS cc_start: 0.8911 (tttt) cc_final: 0.8611 (tttm) REVERT: F 89 GLU cc_start: 0.7819 (mp0) cc_final: 0.7589 (mp0) REVERT: G 13 MET cc_start: 0.8239 (tmm) cc_final: 0.7701 (tmm) REVERT: G 15 LYS cc_start: 0.8751 (mttt) cc_final: 0.8251 (mttm) REVERT: G 34 ARG cc_start: 0.8816 (ttt180) cc_final: 0.8213 (tpp80) REVERT: G 63 GLU cc_start: 0.8518 (pt0) cc_final: 0.7661 (pm20) REVERT: G 66 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7629 (tm-30) REVERT: G 104 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8069 (ttm110) REVERT: H 15 LYS cc_start: 0.8548 (mttt) cc_final: 0.8033 (mtpp) REVERT: H 34 ARG cc_start: 0.9024 (ttt180) cc_final: 0.8406 (tpp80) REVERT: H 62 GLU cc_start: 0.7841 (mp0) cc_final: 0.7480 (mp0) REVERT: H 63 GLU cc_start: 0.8634 (pt0) cc_final: 0.7886 (pm20) REVERT: H 66 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7630 (tm-30) REVERT: I 13 MET cc_start: 0.7991 (tmm) cc_final: 0.7745 (tmm) REVERT: I 15 LYS cc_start: 0.8547 (mttt) cc_final: 0.7962 (mtpp) REVERT: I 34 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8430 (tpp80) REVERT: I 62 GLU cc_start: 0.8026 (mp0) cc_final: 0.7707 (mp0) REVERT: I 63 GLU cc_start: 0.8474 (pt0) cc_final: 0.8251 (pt0) REVERT: I 80 LYS cc_start: 0.8845 (tttt) cc_final: 0.8497 (tttp) REVERT: I 89 GLU cc_start: 0.7948 (mp0) cc_final: 0.7701 (pm20) REVERT: I 99 ASP cc_start: 0.8863 (t0) cc_final: 0.8353 (t70) REVERT: I 100 SER cc_start: 0.8697 (t) cc_final: 0.8387 (p) REVERT: I 104 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7739 (ttm110) REVERT: J 13 MET cc_start: 0.8254 (tmm) cc_final: 0.7714 (tmm) REVERT: J 15 LYS cc_start: 0.8514 (mttt) cc_final: 0.7880 (ttmm) REVERT: J 21 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8078 (mmm160) REVERT: J 34 ARG cc_start: 0.8521 (ttt180) cc_final: 0.7804 (tpp80) REVERT: J 35 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8714 (ttmm) REVERT: J 62 GLU cc_start: 0.8135 (mp0) cc_final: 0.7846 (mp0) REVERT: J 63 GLU cc_start: 0.8497 (pt0) cc_final: 0.8058 (pt0) REVERT: J 66 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7789 (tm-30) REVERT: J 72 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8483 (mm-30) REVERT: J 84 ILE cc_start: 0.9337 (mt) cc_final: 0.8766 (pp) REVERT: J 89 GLU cc_start: 0.7896 (mp0) cc_final: 0.7679 (mp0) REVERT: J 100 SER cc_start: 0.8929 (t) cc_final: 0.8566 (p) REVERT: K 15 LYS cc_start: 0.8539 (mttt) cc_final: 0.7959 (mtpm) REVERT: K 21 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8200 (mtp85) REVERT: K 30 MET cc_start: 0.7941 (ppp) cc_final: 0.7694 (ppp) REVERT: K 35 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8769 (ttmt) REVERT: K 62 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7787 (mp0) REVERT: K 63 GLU cc_start: 0.8692 (pt0) cc_final: 0.8390 (pt0) REVERT: K 80 LYS cc_start: 0.8923 (tttt) cc_final: 0.8512 (tttp) REVERT: K 84 ILE cc_start: 0.9498 (mt) cc_final: 0.9293 (mp) REVERT: K 90 HIS cc_start: 0.8709 (m90) cc_final: 0.8446 (m90) REVERT: K 99 ASP cc_start: 0.8486 (t0) cc_final: 0.8053 (t70) REVERT: K 100 SER cc_start: 0.8914 (t) cc_final: 0.8644 (p) REVERT: K 118 THR cc_start: 0.9212 (m) cc_final: 0.8874 (p) outliers start: 36 outliers final: 6 residues processed: 381 average time/residue: 1.3345 time to fit residues: 533.9752 Evaluate side-chains 354 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 343 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER 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 I residue 82 LEU Chi-restraints excluded: chain J residue 72 GLU Chi-restraints excluded: chain K residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.070221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.050073 restraints weight = 17895.608| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.73 r_work: 0.3143 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 8096 Z= 0.483 Angle : 0.784 8.889 11000 Z= 0.410 Chirality : 0.053 0.144 1287 Planarity : 0.005 0.048 1353 Dihedral : 5.983 24.804 1089 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 79 HIS 0.006 0.002 HIS H 90 PHE 0.025 0.002 PHE K 64 TYR 0.021 0.003 TYR K 105 ARG 0.012 0.001 ARG F 104 *********************** 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 376 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 0.914 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: 0.8656 (ttt180) cc_final: 0.8018 (tpp80) REVERT: A 63 GLU cc_start: 0.8887 (pt0) cc_final: 0.8254 (pp20) REVERT: A 66 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 70 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8711 (tppp) REVERT: A 90 HIS cc_start: 0.8339 (m90) cc_final: 0.7912 (m90) REVERT: A 92 GLU cc_start: 0.7721 (mp0) cc_final: 0.7375 (mp0) REVERT: A 104 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7222 (mtm-85) REVERT: B 13 MET cc_start: 0.7919 (tmm) cc_final: 0.7552 (tmm) REVERT: B 15 LYS cc_start: 0.8568 (mttt) cc_final: 0.7894 (mtpm) REVERT: B 21 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7908 (tpp80) REVERT: B 34 ARG cc_start: 0.8742 (ttt180) cc_final: 0.8047 (tpp80) REVERT: B 61 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 62 GLU cc_start: 0.7854 (mp0) cc_final: 0.7273 (mp0) REVERT: B 66 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7367 (tm-30) REVERT: B 80 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8647 (ttpt) REVERT: B 90 HIS cc_start: 0.8253 (m90) cc_final: 0.7843 (m90) REVERT: B 92 GLU cc_start: 0.7202 (mp0) cc_final: 0.6861 (mp0) REVERT: B 104 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: C 15 LYS cc_start: 0.8638 (mttt) cc_final: 0.8116 (mtpm) REVERT: C 18 ASP cc_start: 0.8958 (m-30) cc_final: 0.8605 (m-30) REVERT: C 63 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: C 66 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 90 HIS cc_start: 0.8399 (m90) cc_final: 0.8154 (m90) REVERT: D 13 MET cc_start: 0.8043 (tmm) cc_final: 0.7645 (tmm) REVERT: D 34 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8509 (tpp80) REVERT: D 62 GLU cc_start: 0.7883 (mp0) cc_final: 0.7625 (mp0) REVERT: D 66 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7899 (tm-30) REVERT: D 80 LYS cc_start: 0.8949 (tttt) cc_final: 0.8609 (tttm) REVERT: E 13 MET cc_start: 0.8327 (tmm) cc_final: 0.7988 (tmm) REVERT: E 21 ARG cc_start: 0.8460 (tpt-90) cc_final: 0.7976 (mmm160) REVERT: E 26 ILE cc_start: 0.9153 (mt) cc_final: 0.8895 (mp) REVERT: E 30 MET cc_start: 0.7708 (tmm) cc_final: 0.6867 (tmm) REVERT: E 34 ARG cc_start: 0.8923 (ttt180) cc_final: 0.8371 (tpp80) REVERT: E 62 GLU cc_start: 0.8360 (pm20) cc_final: 0.7934 (pm20) REVERT: E 66 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7963 (tm-30) REVERT: E 116 TYR cc_start: 0.9380 (m-80) cc_final: 0.9155 (m-80) REVERT: F 13 MET cc_start: 0.8066 (tmm) cc_final: 0.7470 (tmm) REVERT: F 15 LYS cc_start: 0.8741 (mttt) cc_final: 0.8186 (mtpm) REVERT: F 18 ASP cc_start: 0.8964 (m-30) cc_final: 0.8689 (m-30) REVERT: F 30 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8001 (tmm) REVERT: F 34 ARG cc_start: 0.8977 (ttt180) cc_final: 0.8274 (tpp80) REVERT: F 35 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8803 (ttmm) REVERT: F 62 GLU cc_start: 0.8087 (pm20) cc_final: 0.7855 (pm20) REVERT: F 63 GLU cc_start: 0.7905 (pm20) cc_final: 0.7210 (pm20) REVERT: F 66 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7704 (tm-30) REVERT: F 72 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8661 (mt-10) REVERT: F 80 LYS cc_start: 0.8958 (tttt) cc_final: 0.8640 (tttm) REVERT: F 84 ILE cc_start: 0.9303 (mm) cc_final: 0.8855 (pp) REVERT: F 89 GLU cc_start: 0.7748 (mp0) cc_final: 0.7429 (mp0) REVERT: G 13 MET cc_start: 0.8559 (tmm) cc_final: 0.7900 (tmm) REVERT: G 15 LYS cc_start: 0.8931 (mttt) cc_final: 0.8310 (mttm) REVERT: G 34 ARG cc_start: 0.8838 (ttt180) cc_final: 0.8239 (tpp80) REVERT: G 35 LYS cc_start: 0.9053 (tppt) cc_final: 0.8848 (tppt) REVERT: G 61 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7914 (mt-10) REVERT: G 63 GLU cc_start: 0.8501 (pt0) cc_final: 0.7656 (pm20) REVERT: G 66 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7617 (tm-30) REVERT: G 104 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8155 (ttm110) REVERT: H 15 LYS cc_start: 0.8615 (mttt) cc_final: 0.8240 (mtpt) REVERT: H 34 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8355 (tpp80) REVERT: H 62 GLU cc_start: 0.8169 (mp0) cc_final: 0.7516 (mp0) REVERT: H 63 GLU cc_start: 0.8734 (pt0) cc_final: 0.7974 (pm20) REVERT: H 66 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7849 (tm-30) REVERT: I 13 MET cc_start: 0.8075 (tmm) cc_final: 0.7689 (tmm) REVERT: I 15 LYS cc_start: 0.8778 (mttt) cc_final: 0.8197 (mtpp) REVERT: I 30 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: I 34 ARG cc_start: 0.8751 (ttt180) cc_final: 0.8358 (tpp80) REVERT: I 62 GLU cc_start: 0.8134 (mp0) cc_final: 0.7896 (mm-30) REVERT: I 70 LYS cc_start: 0.9351 (ttmm) cc_final: 0.8979 (ttpp) REVERT: I 80 LYS cc_start: 0.8887 (tttt) cc_final: 0.8533 (tttm) REVERT: I 99 ASP cc_start: 0.9127 (t0) cc_final: 0.8502 (t70) REVERT: I 100 SER cc_start: 0.8774 (t) cc_final: 0.8488 (p) REVERT: I 104 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7872 (ttm110) REVERT: J 13 MET cc_start: 0.8433 (tmm) cc_final: 0.8039 (tmm) REVERT: J 21 ARG cc_start: 0.8435 (mmm160) cc_final: 0.8201 (mmm160) REVERT: J 34 ARG cc_start: 0.8583 (ttt180) cc_final: 0.7896 (tpp80) REVERT: J 63 GLU cc_start: 0.8538 (pt0) cc_final: 0.8197 (pt0) REVERT: J 66 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7510 (tm-30) REVERT: J 84 ILE cc_start: 0.9281 (mt) cc_final: 0.8742 (pp) REVERT: J 89 GLU cc_start: 0.7808 (mp0) cc_final: 0.7594 (mp0) REVERT: J 100 SER cc_start: 0.8992 (t) cc_final: 0.8650 (p) REVERT: K 13 MET cc_start: 0.8108 (tmm) cc_final: 0.7585 (tmt) REVERT: K 15 LYS cc_start: 0.8478 (mttt) cc_final: 0.7887 (mtpm) REVERT: K 21 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8215 (mtp85) REVERT: K 62 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7608 (mp0) REVERT: K 63 GLU cc_start: 0.8703 (pt0) cc_final: 0.8434 (pt0) REVERT: K 66 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8294 (tm-30) REVERT: K 80 LYS cc_start: 0.8911 (tttt) cc_final: 0.8486 (tttp) REVERT: K 90 HIS cc_start: 0.8662 (m90) cc_final: 0.8315 (m90) REVERT: K 99 ASP cc_start: 0.8487 (t0) cc_final: 0.8216 (t70) REVERT: K 100 SER cc_start: 0.8938 (t) cc_final: 0.8677 (p) REVERT: K 118 THR cc_start: 0.9182 (m) cc_final: 0.8797 (p) outliers start: 38 outliers final: 16 residues processed: 354 average time/residue: 1.3639 time to fit residues: 505.8929 Evaluate side-chains 339 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 318 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE 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 D residue 30 MET Chi-restraints excluded: chain E residue 58 LEU 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 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain K residue 68 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3864 r_free = 0.3864 target = 0.071813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051821 restraints weight = 17169.033| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.67 r_work: 0.3283 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8096 Z= 0.309 Angle : 0.761 9.330 11000 Z= 0.389 Chirality : 0.052 0.154 1287 Planarity : 0.005 0.045 1353 Dihedral : 5.797 23.416 1089 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.24 % Allowed : 22.73 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.005 0.001 HIS C 88 PHE 0.028 0.002 PHE K 64 TYR 0.022 0.002 TYR K 114 ARG 0.013 0.002 ARG F 104 *********************** 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 389 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 344 time to evaluate : 0.873 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: 0.8741 (ttt180) cc_final: 0.8194 (tpp80) REVERT: A 63 GLU cc_start: 0.8889 (pt0) cc_final: 0.8180 (pp20) REVERT: A 66 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 70 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8831 (tppp) REVERT: A 89 GLU cc_start: 0.7533 (pm20) cc_final: 0.6477 (pm20) REVERT: A 90 HIS cc_start: 0.8400 (m90) cc_final: 0.7858 (m90) REVERT: A 92 GLU cc_start: 0.7878 (mp0) cc_final: 0.7554 (mp0) REVERT: A 104 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7183 (mtm-85) REVERT: A 106 THR cc_start: 0.9193 (m) cc_final: 0.8809 (t) REVERT: B 13 MET cc_start: 0.8033 (tmm) cc_final: 0.7755 (tmm) REVERT: B 15 LYS cc_start: 0.8663 (mttt) cc_final: 0.7914 (mtpm) REVERT: B 34 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8160 (tpp80) REVERT: B 35 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8882 (mtpp) REVERT: B 61 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 62 GLU cc_start: 0.7771 (mp0) cc_final: 0.7192 (mp0) REVERT: B 66 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7161 (tm-30) REVERT: B 69 TYR cc_start: 0.9399 (m-80) cc_final: 0.9193 (m-80) REVERT: B 80 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8664 (ttpt) REVERT: B 90 HIS cc_start: 0.8310 (m90) cc_final: 0.7876 (m90) REVERT: B 92 GLU cc_start: 0.7192 (mp0) cc_final: 0.6857 (mp0) REVERT: B 104 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: C 15 LYS cc_start: 0.8638 (mttt) cc_final: 0.8105 (mtpm) REVERT: C 18 ASP cc_start: 0.8974 (m-30) cc_final: 0.8430 (m-30) REVERT: C 30 MET cc_start: 0.8449 (ttm) cc_final: 0.7847 (tmm) REVERT: C 35 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8939 (ttmt) REVERT: C 63 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: C 66 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: C 90 HIS cc_start: 0.8523 (m90) cc_final: 0.8278 (m90) REVERT: D 13 MET cc_start: 0.8084 (tmm) cc_final: 0.7582 (tmm) REVERT: D 15 LYS cc_start: 0.8635 (mttt) cc_final: 0.8009 (mtpm) REVERT: D 34 ARG cc_start: 0.9033 (ttt180) cc_final: 0.8507 (tpp80) REVERT: D 62 GLU cc_start: 0.7924 (mp0) cc_final: 0.7608 (mp0) REVERT: D 63 GLU cc_start: 0.7868 (pm20) cc_final: 0.7645 (pm20) REVERT: D 66 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 80 LYS cc_start: 0.8982 (tttt) cc_final: 0.8630 (tttm) REVERT: D 104 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.8055 (ttm110) REVERT: D 116 TYR cc_start: 0.9467 (m-80) cc_final: 0.9241 (m-80) REVERT: E 13 MET cc_start: 0.8353 (tmm) cc_final: 0.8003 (tmm) REVERT: E 30 MET cc_start: 0.7935 (tmm) cc_final: 0.7413 (tmm) REVERT: E 34 ARG cc_start: 0.8966 (ttt180) cc_final: 0.8390 (tpp80) REVERT: E 62 GLU cc_start: 0.8427 (pm20) cc_final: 0.8042 (pm20) REVERT: E 66 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7701 (tm-30) REVERT: E 72 GLU cc_start: 0.8956 (mt-10) cc_final: 0.7508 (mp0) REVERT: E 116 TYR cc_start: 0.9394 (m-80) cc_final: 0.9124 (m-80) REVERT: F 13 MET cc_start: 0.8139 (tmm) cc_final: 0.7590 (tmm) REVERT: F 15 LYS cc_start: 0.8756 (mttt) cc_final: 0.8147 (mtpm) REVERT: F 18 ASP cc_start: 0.8925 (m-30) cc_final: 0.8609 (m-30) REVERT: F 30 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7893 (tmm) REVERT: F 34 ARG cc_start: 0.8988 (ttt180) cc_final: 0.8282 (tpp80) REVERT: F 35 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8860 (ttmm) REVERT: F 62 GLU cc_start: 0.8201 (pm20) cc_final: 0.7893 (pm20) REVERT: F 63 GLU cc_start: 0.7892 (pm20) cc_final: 0.7261 (pm20) REVERT: F 66 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7772 (tm-30) REVERT: F 70 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9033 (ptmm) REVERT: F 80 LYS cc_start: 0.8951 (tttt) cc_final: 0.8634 (tttm) REVERT: F 84 ILE cc_start: 0.9363 (mm) cc_final: 0.8879 (pp) REVERT: F 89 GLU cc_start: 0.7853 (mp0) cc_final: 0.7496 (mp0) REVERT: G 13 MET cc_start: 0.8648 (tmm) cc_final: 0.7796 (tmm) REVERT: G 15 LYS cc_start: 0.8981 (mttt) cc_final: 0.8297 (mttp) REVERT: G 30 MET cc_start: 0.7921 (tmm) cc_final: 0.7625 (tmm) REVERT: G 34 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8276 (tpp80) REVERT: G 61 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7956 (mt-10) REVERT: G 63 GLU cc_start: 0.8510 (pt0) cc_final: 0.7597 (pm20) REVERT: G 66 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 104 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8105 (ttm110) REVERT: H 15 LYS cc_start: 0.8685 (mttt) cc_final: 0.8207 (mtpp) REVERT: H 34 ARG cc_start: 0.8986 (ttt180) cc_final: 0.8359 (tpp80) REVERT: H 62 GLU cc_start: 0.8257 (mp0) cc_final: 0.7552 (mp0) REVERT: H 63 GLU cc_start: 0.8719 (pt0) cc_final: 0.7939 (pm20) REVERT: H 66 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7635 (tm-30) REVERT: I 13 MET cc_start: 0.8036 (tmm) cc_final: 0.7579 (tmm) REVERT: I 15 LYS cc_start: 0.8758 (mttt) cc_final: 0.8165 (ttmm) REVERT: I 30 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: I 34 ARG cc_start: 0.8777 (ttt180) cc_final: 0.8376 (tpp80) REVERT: I 62 GLU cc_start: 0.8183 (mp0) cc_final: 0.7981 (mp0) REVERT: I 80 LYS cc_start: 0.8879 (tttt) cc_final: 0.8517 (tttm) REVERT: I 99 ASP cc_start: 0.9073 (t0) cc_final: 0.8475 (t70) REVERT: I 100 SER cc_start: 0.8759 (t) cc_final: 0.8455 (p) REVERT: I 104 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7844 (ttm110) REVERT: J 13 MET cc_start: 0.8497 (tmm) cc_final: 0.8150 (tmm) REVERT: J 15 LYS cc_start: 0.8603 (mttt) cc_final: 0.7856 (ttmm) REVERT: J 21 ARG cc_start: 0.8378 (mmm160) cc_final: 0.8166 (mmm160) REVERT: J 34 ARG cc_start: 0.8619 (ttt180) cc_final: 0.7942 (tpp80) REVERT: J 61 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: J 63 GLU cc_start: 0.8623 (pt0) cc_final: 0.8322 (pt0) REVERT: J 66 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7645 (tm-30) REVERT: J 84 ILE cc_start: 0.9338 (mt) cc_final: 0.8813 (pp) REVERT: J 89 GLU cc_start: 0.7903 (mp0) cc_final: 0.7623 (mp0) REVERT: J 100 SER cc_start: 0.8973 (t) cc_final: 0.8614 (p) REVERT: K 13 MET cc_start: 0.8132 (tmm) cc_final: 0.7852 (tmm) REVERT: K 15 LYS cc_start: 0.8532 (mttt) cc_final: 0.7938 (mtpm) REVERT: K 21 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8293 (mtp85) REVERT: K 58 LEU cc_start: 0.8785 (mt) cc_final: 0.8553 (tp) REVERT: K 62 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7764 (mp0) REVERT: K 63 GLU cc_start: 0.8785 (pt0) cc_final: 0.8572 (pt0) REVERT: K 66 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8282 (tm-30) REVERT: K 80 LYS cc_start: 0.8900 (tttt) cc_final: 0.8505 (tttm) REVERT: K 90 HIS cc_start: 0.8801 (m90) cc_final: 0.8599 (m90) REVERT: K 99 ASP cc_start: 0.8498 (t0) cc_final: 0.8209 (t70) REVERT: K 118 THR cc_start: 0.9220 (m) cc_final: 0.8857 (p) outliers start: 45 outliers final: 18 residues processed: 362 average time/residue: 1.4620 time to fit residues: 555.1248 Evaluate side-chains 353 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 E residue 58 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR 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 26 ILE 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 68 ILE 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 30 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN K 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.071673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051819 restraints weight = 17161.882| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.67 r_work: 0.3298 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8096 Z= 0.297 Angle : 0.763 9.941 11000 Z= 0.387 Chirality : 0.052 0.200 1287 Planarity : 0.005 0.050 1353 Dihedral : 5.684 23.135 1089 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.83 % Allowed : 23.08 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS C 88 PHE 0.025 0.002 PHE K 64 TYR 0.021 0.002 TYR K 114 ARG 0.016 0.002 ARG F 104 *********************** 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 399 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8202 (tpp80) REVERT: A 61 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 63 GLU cc_start: 0.8890 (pt0) cc_final: 0.8170 (pp20) REVERT: A 66 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 70 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8842 (tppp) REVERT: A 89 GLU cc_start: 0.7993 (pm20) cc_final: 0.7684 (pm20) REVERT: A 90 HIS cc_start: 0.8452 (m90) cc_final: 0.7948 (m90) REVERT: A 92 GLU cc_start: 0.7826 (mp0) cc_final: 0.7619 (mp0) REVERT: A 104 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7742 (mtt90) REVERT: A 106 THR cc_start: 0.9192 (m) cc_final: 0.8819 (t) REVERT: B 13 MET cc_start: 0.8112 (tmm) cc_final: 0.7689 (tmm) REVERT: B 15 LYS cc_start: 0.8664 (mttt) cc_final: 0.7854 (mtpm) REVERT: B 21 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7998 (tpp80) REVERT: B 34 ARG cc_start: 0.8774 (ttt180) cc_final: 0.8150 (tpp80) REVERT: B 35 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8834 (mtpp) REVERT: B 61 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 62 GLU cc_start: 0.7794 (mp0) cc_final: 0.7224 (mp0) REVERT: B 63 GLU cc_start: 0.7852 (pm20) cc_final: 0.7626 (pm20) REVERT: B 66 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 69 TYR cc_start: 0.9410 (m-80) cc_final: 0.9126 (m-80) REVERT: B 80 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8661 (ttpt) REVERT: B 84 ILE cc_start: 0.9336 (mp) cc_final: 0.9127 (pp) REVERT: B 90 HIS cc_start: 0.8359 (m90) cc_final: 0.7961 (m90) REVERT: C 15 LYS cc_start: 0.8668 (mttt) cc_final: 0.8131 (mtpm) REVERT: C 18 ASP cc_start: 0.8948 (m-30) cc_final: 0.8387 (m-30) REVERT: C 30 MET cc_start: 0.8484 (ttm) cc_final: 0.8053 (tmm) REVERT: C 35 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8907 (ttmm) REVERT: C 62 GLU cc_start: 0.8053 (mp0) cc_final: 0.7778 (mp0) REVERT: C 63 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: C 90 HIS cc_start: 0.8596 (m90) cc_final: 0.8224 (m90) REVERT: D 13 MET cc_start: 0.8105 (tmm) cc_final: 0.7636 (tmm) REVERT: D 15 LYS cc_start: 0.8630 (mttt) cc_final: 0.8002 (mtpm) REVERT: D 34 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8477 (tpp80) REVERT: D 61 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: D 62 GLU cc_start: 0.7978 (mp0) cc_final: 0.7469 (mp0) REVERT: D 66 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7671 (tm-30) REVERT: D 80 LYS cc_start: 0.8976 (tttt) cc_final: 0.8622 (tttm) REVERT: D 104 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8008 (mtm-85) REVERT: E 13 MET cc_start: 0.8363 (tmm) cc_final: 0.8016 (tmm) REVERT: E 30 MET cc_start: 0.8048 (tmm) cc_final: 0.7512 (tmm) REVERT: E 34 ARG cc_start: 0.8938 (ttt180) cc_final: 0.8404 (tpp80) REVERT: E 62 GLU cc_start: 0.8448 (pm20) cc_final: 0.7413 (mp0) REVERT: E 66 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7737 (tm-30) REVERT: E 72 GLU cc_start: 0.8899 (mt-10) cc_final: 0.7698 (mp0) REVERT: E 116 TYR cc_start: 0.9363 (m-80) cc_final: 0.9039 (m-80) REVERT: F 13 MET cc_start: 0.8166 (tmm) cc_final: 0.7772 (tmm) REVERT: F 15 LYS cc_start: 0.8734 (mttt) cc_final: 0.8055 (mtpm) REVERT: F 18 ASP cc_start: 0.8901 (m-30) cc_final: 0.8535 (m-30) REVERT: F 30 MET cc_start: 0.8351 (ttm) cc_final: 0.7875 (tmm) REVERT: F 34 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8278 (tpp80) REVERT: F 35 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8867 (ttmm) REVERT: F 62 GLU cc_start: 0.8183 (pm20) cc_final: 0.7677 (pm20) REVERT: F 63 GLU cc_start: 0.7921 (pm20) cc_final: 0.7201 (pm20) REVERT: F 66 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7543 (tm-30) REVERT: F 69 TYR cc_start: 0.9307 (m-80) cc_final: 0.9074 (m-80) REVERT: F 70 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8878 (ptmm) REVERT: F 72 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: F 80 LYS cc_start: 0.8948 (tttt) cc_final: 0.8627 (tttm) REVERT: F 89 GLU cc_start: 0.7821 (mp0) cc_final: 0.7571 (mp0) REVERT: G 13 MET cc_start: 0.8623 (tmm) cc_final: 0.7812 (tmm) REVERT: G 15 LYS cc_start: 0.8989 (mttt) cc_final: 0.8335 (mttm) REVERT: G 30 MET cc_start: 0.8147 (tmm) cc_final: 0.7314 (tmm) REVERT: G 34 ARG cc_start: 0.8905 (ttt180) cc_final: 0.8315 (tpp80) REVERT: G 63 GLU cc_start: 0.8535 (pt0) cc_final: 0.7564 (pm20) REVERT: G 66 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7517 (tm-30) REVERT: G 104 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8071 (ttm110) REVERT: H 15 LYS cc_start: 0.8678 (mttt) cc_final: 0.7964 (mtpp) REVERT: H 30 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7824 (tmm) REVERT: H 34 ARG cc_start: 0.8970 (ttt180) cc_final: 0.8335 (tpp80) REVERT: H 62 GLU cc_start: 0.8318 (mp0) cc_final: 0.7767 (mp0) REVERT: H 63 GLU cc_start: 0.8734 (pt0) cc_final: 0.8005 (pm20) REVERT: H 66 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7650 (tm-30) REVERT: I 13 MET cc_start: 0.8078 (tmm) cc_final: 0.7680 (tmm) REVERT: I 15 LYS cc_start: 0.8748 (mttt) cc_final: 0.7949 (mtpp) REVERT: I 18 ASP cc_start: 0.8846 (m-30) cc_final: 0.8633 (m-30) REVERT: I 30 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: I 34 ARG cc_start: 0.8765 (ttt180) cc_final: 0.8388 (tpp80) REVERT: I 62 GLU cc_start: 0.8203 (mp0) cc_final: 0.7982 (mp0) REVERT: I 72 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8455 (mp0) REVERT: I 80 LYS cc_start: 0.8884 (tttt) cc_final: 0.8521 (tttm) REVERT: I 99 ASP cc_start: 0.8938 (t0) cc_final: 0.8375 (t70) REVERT: I 100 SER cc_start: 0.8789 (t) cc_final: 0.8509 (p) REVERT: I 104 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7813 (ttm110) REVERT: J 13 MET cc_start: 0.8458 (tmm) cc_final: 0.8109 (tmm) REVERT: J 15 LYS cc_start: 0.8577 (mttt) cc_final: 0.7851 (ttmm) REVERT: J 21 ARG cc_start: 0.8381 (mmm160) cc_final: 0.8168 (mmm160) REVERT: J 34 ARG cc_start: 0.8611 (ttt180) cc_final: 0.7981 (tpp80) REVERT: J 35 LYS cc_start: 0.8982 (ttmm) cc_final: 0.8676 (mtpt) REVERT: J 63 GLU cc_start: 0.8639 (pt0) cc_final: 0.8379 (pt0) REVERT: J 66 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7591 (tm-30) REVERT: J 84 ILE cc_start: 0.9331 (mt) cc_final: 0.8800 (pp) REVERT: J 89 GLU cc_start: 0.7756 (mp0) cc_final: 0.7487 (mp0) REVERT: J 100 SER cc_start: 0.8915 (t) cc_final: 0.8521 (p) REVERT: K 13 MET cc_start: 0.8180 (tmm) cc_final: 0.7915 (tmm) REVERT: K 15 LYS cc_start: 0.8500 (mttt) cc_final: 0.7910 (mtpm) REVERT: K 21 ARG cc_start: 0.8542 (mmm-85) cc_final: 0.8316 (mtp85) REVERT: K 62 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7847 (mp0) REVERT: K 63 GLU cc_start: 0.8811 (pt0) cc_final: 0.8611 (pt0) REVERT: K 66 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8306 (tm-30) REVERT: K 73 ILE cc_start: 0.8448 (mt) cc_final: 0.8028 (mp) REVERT: K 80 LYS cc_start: 0.8890 (tttt) cc_final: 0.8492 (tttm) REVERT: K 99 ASP cc_start: 0.8483 (t0) cc_final: 0.8211 (t70) REVERT: K 118 THR cc_start: 0.9198 (m) cc_final: 0.8779 (p) outliers start: 50 outliers final: 20 residues processed: 368 average time/residue: 1.4070 time to fit residues: 543.3373 Evaluate side-chains 360 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 333 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE 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 C residue 96 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F 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 70 LYS Chi-restraints excluded: chain H residue 30 MET 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 26 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 59 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.069768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.050198 restraints weight = 17472.593| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.63 r_work: 0.3243 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8096 Z= 0.412 Angle : 0.818 10.057 11000 Z= 0.414 Chirality : 0.053 0.193 1287 Planarity : 0.005 0.052 1353 Dihedral : 5.831 25.921 1089 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.94 % Allowed : 24.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.005 0.001 HIS C 88 PHE 0.026 0.002 PHE K 64 TYR 0.024 0.002 TYR A 105 ARG 0.017 0.002 ARG F 104 *********************** 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 387 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 336 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8202 (tpp80) REVERT: A 63 GLU cc_start: 0.8871 (pt0) cc_final: 0.8177 (pp20) REVERT: A 66 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 70 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8831 (tppp) REVERT: A 89 GLU cc_start: 0.8208 (pm20) cc_final: 0.7841 (pm20) REVERT: A 90 HIS cc_start: 0.8403 (m90) cc_final: 0.7908 (m90) REVERT: A 92 GLU cc_start: 0.7782 (mp0) cc_final: 0.7488 (mp0) REVERT: A 104 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: A 106 THR cc_start: 0.9173 (m) cc_final: 0.8758 (t) REVERT: B 13 MET cc_start: 0.8245 (tmm) cc_final: 0.7677 (tmm) REVERT: B 18 ASP cc_start: 0.9082 (m-30) cc_final: 0.8801 (m-30) REVERT: B 21 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8020 (tpp80) REVERT: B 34 ARG cc_start: 0.8796 (ttt180) cc_final: 0.8195 (tpp80) REVERT: B 35 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8854 (mtpp) REVERT: B 61 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 62 GLU cc_start: 0.7844 (mp0) cc_final: 0.7204 (mp0) REVERT: B 66 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7344 (tm-30) REVERT: B 69 TYR cc_start: 0.9410 (m-80) cc_final: 0.9190 (m-80) REVERT: B 80 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8674 (ttpt) REVERT: B 84 ILE cc_start: 0.9386 (mp) cc_final: 0.9102 (pp) REVERT: B 90 HIS cc_start: 0.8353 (m90) cc_final: 0.7992 (m90) REVERT: B 104 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7845 (mtm-85) REVERT: C 15 LYS cc_start: 0.8690 (mttt) cc_final: 0.8134 (mtpm) REVERT: C 18 ASP cc_start: 0.8938 (m-30) cc_final: 0.8509 (m-30) REVERT: C 30 MET cc_start: 0.8516 (ttm) cc_final: 0.8051 (tmm) REVERT: C 35 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8863 (ttmm) REVERT: C 62 GLU cc_start: 0.7936 (mp0) cc_final: 0.7573 (mp0) REVERT: C 63 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: C 66 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: C 84 ILE cc_start: 0.9388 (mm) cc_final: 0.9119 (pp) REVERT: C 90 HIS cc_start: 0.8557 (m90) cc_final: 0.8228 (m90) REVERT: C 104 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7958 (mtm-85) REVERT: D 13 MET cc_start: 0.8158 (tmm) cc_final: 0.7735 (tmm) REVERT: D 15 LYS cc_start: 0.8719 (mttt) cc_final: 0.8089 (mtpm) REVERT: D 34 ARG cc_start: 0.9043 (ttt180) cc_final: 0.8422 (tpp80) REVERT: D 62 GLU cc_start: 0.7921 (mp0) cc_final: 0.7648 (mp0) REVERT: D 63 GLU cc_start: 0.7909 (pm20) cc_final: 0.7310 (pm20) REVERT: D 66 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 80 LYS cc_start: 0.8978 (tttt) cc_final: 0.8632 (tttm) REVERT: D 104 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.7927 (mtm-85) REVERT: D 116 TYR cc_start: 0.9458 (m-80) cc_final: 0.9204 (m-80) REVERT: E 13 MET cc_start: 0.8394 (tmm) cc_final: 0.8053 (tmm) REVERT: E 30 MET cc_start: 0.8198 (tmm) cc_final: 0.7632 (tmm) REVERT: E 34 ARG cc_start: 0.8988 (ttt180) cc_final: 0.8368 (tpp80) REVERT: E 62 GLU cc_start: 0.8498 (pm20) cc_final: 0.7502 (mp0) REVERT: E 63 GLU cc_start: 0.8029 (pm20) cc_final: 0.7816 (pm20) REVERT: E 66 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7670 (tm-30) REVERT: E 116 TYR cc_start: 0.9336 (m-80) cc_final: 0.9055 (m-80) REVERT: F 13 MET cc_start: 0.8239 (tmm) cc_final: 0.7784 (tmm) REVERT: F 15 LYS cc_start: 0.8789 (mttt) cc_final: 0.8035 (mtpm) REVERT: F 18 ASP cc_start: 0.8912 (m-30) cc_final: 0.8524 (m-30) REVERT: F 30 MET cc_start: 0.8412 (ttm) cc_final: 0.7783 (tmm) REVERT: F 34 ARG cc_start: 0.9004 (ttt180) cc_final: 0.8304 (tpp80) REVERT: F 35 LYS cc_start: 0.9214 (ttpt) cc_final: 0.8865 (ttmm) REVERT: F 62 GLU cc_start: 0.8291 (pm20) cc_final: 0.7549 (pm20) REVERT: F 63 GLU cc_start: 0.7940 (pm20) cc_final: 0.7168 (pm20) REVERT: F 66 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7745 (tm-30) REVERT: F 80 LYS cc_start: 0.8959 (tttt) cc_final: 0.8649 (tttp) REVERT: F 89 GLU cc_start: 0.7834 (mp0) cc_final: 0.7472 (mp0) REVERT: G 13 MET cc_start: 0.8686 (tmm) cc_final: 0.7930 (tmm) REVERT: G 15 LYS cc_start: 0.8961 (mttt) cc_final: 0.8340 (mttp) REVERT: G 30 MET cc_start: 0.8246 (tmm) cc_final: 0.7409 (tmm) REVERT: G 34 ARG cc_start: 0.8917 (ttt180) cc_final: 0.8315 (tpp80) REVERT: G 63 GLU cc_start: 0.8545 (pt0) cc_final: 0.7577 (pm20) REVERT: G 66 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 104 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8058 (ttm110) REVERT: H 15 LYS cc_start: 0.8692 (mttt) cc_final: 0.7980 (mtpp) REVERT: H 30 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7856 (tmm) REVERT: H 34 ARG cc_start: 0.8951 (ttt180) cc_final: 0.8318 (tpp80) REVERT: H 61 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7974 (mt-10) REVERT: H 62 GLU cc_start: 0.8378 (mp0) cc_final: 0.7791 (mp0) REVERT: H 63 GLU cc_start: 0.8785 (pt0) cc_final: 0.8038 (pm20) REVERT: H 66 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7753 (tm-30) REVERT: H 84 ILE cc_start: 0.9355 (mt) cc_final: 0.8856 (pp) REVERT: I 13 MET cc_start: 0.8120 (tmm) cc_final: 0.7636 (tmm) REVERT: I 15 LYS cc_start: 0.8753 (mttt) cc_final: 0.7943 (mtpp) REVERT: I 30 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: I 34 ARG cc_start: 0.8804 (ttt180) cc_final: 0.8437 (tpp80) REVERT: I 70 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.8666 (ttpp) REVERT: I 72 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8217 (mp0) REVERT: I 80 LYS cc_start: 0.8882 (tttt) cc_final: 0.8523 (tttm) REVERT: I 99 ASP cc_start: 0.8912 (t0) cc_final: 0.8423 (t70) REVERT: I 100 SER cc_start: 0.8763 (t) cc_final: 0.8492 (p) REVERT: I 104 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7858 (ttm110) REVERT: J 13 MET cc_start: 0.8453 (tmm) cc_final: 0.8122 (tmm) REVERT: J 21 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8196 (mmm160) REVERT: J 30 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: J 34 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8223 (ttt-90) REVERT: J 35 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8662 (mtpp) REVERT: J 63 GLU cc_start: 0.8633 (pt0) cc_final: 0.8394 (pt0) REVERT: J 66 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7529 (tm-30) REVERT: J 84 ILE cc_start: 0.9320 (mt) cc_final: 0.8811 (pp) REVERT: J 100 SER cc_start: 0.8972 (t) cc_final: 0.8620 (p) REVERT: K 13 MET cc_start: 0.8178 (tmm) cc_final: 0.7934 (tmm) REVERT: K 15 LYS cc_start: 0.8460 (mttt) cc_final: 0.7868 (mtpm) REVERT: K 21 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8334 (mtp85) REVERT: K 26 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8954 (mp) REVERT: K 62 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7822 (mp0) REVERT: K 63 GLU cc_start: 0.8793 (pt0) cc_final: 0.8589 (pt0) REVERT: K 66 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8245 (tm-30) REVERT: K 73 ILE cc_start: 0.8387 (mt) cc_final: 0.8010 (mp) REVERT: K 80 LYS cc_start: 0.8884 (tttt) cc_final: 0.8500 (tttm) REVERT: K 99 ASP cc_start: 0.8555 (t0) cc_final: 0.8266 (t70) REVERT: K 118 THR cc_start: 0.9161 (m) cc_final: 0.8659 (p) outliers start: 51 outliers final: 24 residues processed: 362 average time/residue: 1.5395 time to fit residues: 585.4141 Evaluate side-chains 361 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 96 THR 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 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain H residue 30 MET 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 30 MET Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 MET 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 41 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.067706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.049590 restraints weight = 17823.927| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.65 r_work: 0.3234 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 8096 Z= 0.449 Angle : 0.852 11.449 11000 Z= 0.430 Chirality : 0.053 0.237 1287 Planarity : 0.006 0.054 1353 Dihedral : 5.890 24.807 1089 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.66 % Allowed : 26.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (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 TRP 0.005 0.001 TRP E 79 HIS 0.004 0.001 HIS C 88 PHE 0.028 0.002 PHE K 64 TYR 0.022 0.002 TYR I 116 ARG 0.018 0.002 ARG F 104 *********************** 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 373 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8769 (mttt) cc_final: 0.8446 (mtpm) REVERT: A 34 ARG cc_start: 0.8759 (ttt180) cc_final: 0.8174 (tpp80) REVERT: A 63 GLU cc_start: 0.8870 (pt0) cc_final: 0.8172 (pp20) REVERT: A 66 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 70 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8847 (tppp) REVERT: A 84 ILE cc_start: 0.9470 (mt) cc_final: 0.9133 (pp) REVERT: A 89 GLU cc_start: 0.8316 (pm20) cc_final: 0.8053 (pm20) REVERT: A 90 HIS cc_start: 0.8371 (m90) cc_final: 0.7674 (m90) REVERT: A 92 GLU cc_start: 0.7888 (mp0) cc_final: 0.7538 (mp0) REVERT: A 104 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7410 (mtm-85) REVERT: A 106 THR cc_start: 0.9210 (m) cc_final: 0.8830 (p) REVERT: B 13 MET cc_start: 0.8030 (tmm) cc_final: 0.7571 (tmm) REVERT: B 18 ASP cc_start: 0.9085 (m-30) cc_final: 0.8811 (m-30) REVERT: B 21 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8030 (tpp80) REVERT: B 34 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8241 (tpp80) REVERT: B 35 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8885 (mtpp) REVERT: B 61 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 62 GLU cc_start: 0.7909 (mp0) cc_final: 0.7195 (mp0) REVERT: B 66 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 69 TYR cc_start: 0.9417 (m-80) cc_final: 0.9188 (m-80) REVERT: B 80 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8665 (ttpt) REVERT: B 90 HIS cc_start: 0.8250 (m90) cc_final: 0.7958 (m90) REVERT: B 104 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: C 15 LYS cc_start: 0.8687 (mttt) cc_final: 0.8139 (mtpm) REVERT: C 18 ASP cc_start: 0.8942 (m-30) cc_final: 0.8491 (m-30) REVERT: C 30 MET cc_start: 0.8567 (ttm) cc_final: 0.8079 (tmm) REVERT: C 35 LYS cc_start: 0.9225 (ttmt) cc_final: 0.8842 (ttmt) REVERT: C 62 GLU cc_start: 0.7945 (mp0) cc_final: 0.7560 (mp0) REVERT: C 63 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: C 84 ILE cc_start: 0.9453 (mm) cc_final: 0.9168 (pp) REVERT: C 90 HIS cc_start: 0.8529 (m90) cc_final: 0.8208 (m90) REVERT: D 13 MET cc_start: 0.8176 (tmm) cc_final: 0.7730 (tmm) REVERT: D 15 LYS cc_start: 0.8764 (mttt) cc_final: 0.8019 (mtpm) REVERT: D 34 ARG cc_start: 0.9043 (ttt180) cc_final: 0.8403 (tpp80) REVERT: D 62 GLU cc_start: 0.7905 (mp0) cc_final: 0.7650 (mp0) REVERT: D 63 GLU cc_start: 0.7903 (pm20) cc_final: 0.7551 (pm20) REVERT: D 66 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 80 LYS cc_start: 0.8974 (tttt) cc_final: 0.8624 (tttm) REVERT: D 104 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8122 (mtm-85) REVERT: D 116 TYR cc_start: 0.9458 (m-80) cc_final: 0.9228 (m-80) REVERT: E 13 MET cc_start: 0.8418 (tmm) cc_final: 0.8054 (tmm) REVERT: E 15 LYS cc_start: 0.8883 (mttt) cc_final: 0.8298 (mtmt) REVERT: E 30 MET cc_start: 0.8232 (tmm) cc_final: 0.7559 (tmm) REVERT: E 34 ARG cc_start: 0.9001 (ttt180) cc_final: 0.8400 (tpp80) REVERT: E 62 GLU cc_start: 0.8545 (pm20) cc_final: 0.7944 (pm20) REVERT: E 66 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 116 TYR cc_start: 0.9345 (m-80) cc_final: 0.9055 (m-80) REVERT: F 13 MET cc_start: 0.8256 (tmm) cc_final: 0.7689 (tmm) REVERT: F 15 LYS cc_start: 0.8802 (mttt) cc_final: 0.8371 (mtpp) REVERT: F 18 ASP cc_start: 0.8917 (m-30) cc_final: 0.8575 (m-30) REVERT: F 30 MET cc_start: 0.8373 (ttm) cc_final: 0.7815 (tmm) REVERT: F 34 ARG cc_start: 0.9010 (ttt180) cc_final: 0.8315 (tpp80) REVERT: F 35 LYS cc_start: 0.9238 (ttpt) cc_final: 0.8908 (ttmm) REVERT: F 62 GLU cc_start: 0.8344 (pm20) cc_final: 0.7610 (pm20) REVERT: F 63 GLU cc_start: 0.7955 (pm20) cc_final: 0.7146 (pm20) REVERT: F 66 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7807 (tm-30) REVERT: F 80 LYS cc_start: 0.8961 (tttt) cc_final: 0.8648 (tttp) REVERT: G 13 MET cc_start: 0.8661 (tmm) cc_final: 0.7987 (tmm) REVERT: G 15 LYS cc_start: 0.8954 (mttt) cc_final: 0.8371 (mttp) REVERT: G 30 MET cc_start: 0.8406 (tmm) cc_final: 0.7594 (tmm) REVERT: G 34 ARG cc_start: 0.8946 (ttt180) cc_final: 0.8342 (tpp80) REVERT: G 63 GLU cc_start: 0.8542 (pt0) cc_final: 0.7572 (pm20) REVERT: G 66 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 72 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8327 (mp0) REVERT: G 104 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8065 (ttm110) REVERT: H 15 LYS cc_start: 0.8717 (mttt) cc_final: 0.8002 (mtpp) REVERT: H 30 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7839 (tmm) REVERT: H 34 ARG cc_start: 0.8958 (ttt180) cc_final: 0.8322 (tpp80) REVERT: H 62 GLU cc_start: 0.8326 (mp0) cc_final: 0.7873 (mp0) REVERT: H 63 GLU cc_start: 0.8776 (pt0) cc_final: 0.8083 (pm20) REVERT: H 66 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7713 (tm-30) REVERT: H 84 ILE cc_start: 0.9360 (mt) cc_final: 0.8858 (pp) REVERT: I 13 MET cc_start: 0.8169 (tmm) cc_final: 0.7879 (tmm) REVERT: I 15 LYS cc_start: 0.8765 (mttt) cc_final: 0.7968 (mtpm) REVERT: I 18 ASP cc_start: 0.8873 (m-30) cc_final: 0.8635 (m-30) REVERT: I 30 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: I 34 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8365 (tpp80) REVERT: I 80 LYS cc_start: 0.8886 (tttt) cc_final: 0.8514 (tttm) REVERT: I 100 SER cc_start: 0.8768 (t) cc_final: 0.8480 (p) REVERT: I 104 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7882 (ttm110) REVERT: J 13 MET cc_start: 0.8468 (tmm) cc_final: 0.8178 (tmm) REVERT: J 15 LYS cc_start: 0.8632 (mttt) cc_final: 0.7910 (ttmm) REVERT: J 21 ARG cc_start: 0.8418 (mmm160) cc_final: 0.8204 (mmm160) REVERT: J 30 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: J 34 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8255 (ttt-90) REVERT: J 63 GLU cc_start: 0.8676 (pt0) cc_final: 0.8405 (pt0) REVERT: J 66 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7584 (tm-30) REVERT: J 84 ILE cc_start: 0.9355 (mt) cc_final: 0.8844 (pp) REVERT: J 89 GLU cc_start: 0.7852 (mp0) cc_final: 0.7260 (mp0) REVERT: J 100 SER cc_start: 0.8984 (t) cc_final: 0.8640 (p) REVERT: K 13 MET cc_start: 0.8126 (tmm) cc_final: 0.7841 (tmm) REVERT: K 15 LYS cc_start: 0.8442 (mttt) cc_final: 0.7817 (mtpm) REVERT: K 21 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8321 (mtp85) REVERT: K 26 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8949 (mp) REVERT: K 62 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7800 (mp0) REVERT: K 63 GLU cc_start: 0.8785 (pt0) cc_final: 0.8566 (pt0) REVERT: K 66 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8224 (tm-30) REVERT: K 70 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8764 (tptp) REVERT: K 73 ILE cc_start: 0.8375 (mt) cc_final: 0.8002 (mp) REVERT: K 80 LYS cc_start: 0.8883 (tttt) cc_final: 0.8501 (tttm) REVERT: K 99 ASP cc_start: 0.8572 (t0) cc_final: 0.8265 (t70) outliers start: 40 outliers final: 22 residues processed: 354 average time/residue: 1.7519 time to fit residues: 652.4102 Evaluate side-chains 355 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 326 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 96 THR 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 30 MET 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 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 MET 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 70 LYS 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 69 optimal weight: 0.9980 chunk 95 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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 K 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.072001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.053274 restraints weight = 17060.470| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.66 r_work: 0.3327 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8096 Z= 0.249 Angle : 0.839 9.907 11000 Z= 0.420 Chirality : 0.052 0.158 1287 Planarity : 0.006 0.071 1353 Dihedral : 5.757 23.257 1089 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.08 % Allowed : 27.97 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP G 79 HIS 0.003 0.001 HIS J 31 PHE 0.030 0.001 PHE K 64 TYR 0.019 0.002 TYR K 114 ARG 0.018 0.002 ARG F 104 *********************** 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 392 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 357 time to evaluate : 0.998 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: 0.8840 (ttt180) cc_final: 0.8232 (tpp80) REVERT: A 63 GLU cc_start: 0.8909 (pt0) cc_final: 0.8123 (pp20) REVERT: A 66 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 70 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8878 (tppp) REVERT: A 84 ILE cc_start: 0.9514 (mt) cc_final: 0.9163 (pp) REVERT: A 90 HIS cc_start: 0.8537 (m90) cc_final: 0.7883 (m90) REVERT: A 92 GLU cc_start: 0.8034 (mp0) cc_final: 0.7697 (mp0) REVERT: A 104 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7449 (mtm-85) REVERT: A 106 THR cc_start: 0.9265 (m) cc_final: 0.8951 (p) REVERT: B 13 MET cc_start: 0.8073 (tmm) cc_final: 0.7634 (tmm) REVERT: B 15 LYS cc_start: 0.8644 (mttt) cc_final: 0.7824 (mtpm) REVERT: B 34 ARG cc_start: 0.8798 (ttt180) cc_final: 0.8281 (tpp80) REVERT: B 61 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7709 (mt-10) REVERT: B 62 GLU cc_start: 0.7951 (mp0) cc_final: 0.7335 (mp0) REVERT: B 66 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 80 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8631 (ttpt) REVERT: B 104 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7597 (mtm-85) REVERT: C 15 LYS cc_start: 0.8676 (mttt) cc_final: 0.8175 (mtpm) REVERT: C 18 ASP cc_start: 0.8929 (m-30) cc_final: 0.8482 (m-30) REVERT: C 30 MET cc_start: 0.8467 (ttm) cc_final: 0.8083 (tmm) REVERT: C 35 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8913 (ttmt) REVERT: C 62 GLU cc_start: 0.7915 (mp0) cc_final: 0.7572 (mp0) REVERT: C 63 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: C 90 HIS cc_start: 0.8600 (m90) cc_final: 0.8169 (m90) REVERT: D 13 MET cc_start: 0.8137 (tmm) cc_final: 0.7646 (tmm) REVERT: D 15 LYS cc_start: 0.8676 (mttt) cc_final: 0.8053 (mtpm) REVERT: D 34 ARG cc_start: 0.9032 (ttt180) cc_final: 0.8409 (tpp80) REVERT: D 58 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8496 (tp) REVERT: D 62 GLU cc_start: 0.7904 (mp0) cc_final: 0.7606 (mp0) REVERT: D 63 GLU cc_start: 0.7924 (pm20) cc_final: 0.7593 (pm20) REVERT: D 66 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 80 LYS cc_start: 0.8983 (tttt) cc_final: 0.8620 (tttm) REVERT: D 104 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8081 (mtm-85) REVERT: D 116 TYR cc_start: 0.9473 (m-80) cc_final: 0.9158 (m-80) REVERT: E 13 MET cc_start: 0.8413 (tmm) cc_final: 0.8043 (tmm) REVERT: E 30 MET cc_start: 0.8366 (tmm) cc_final: 0.7616 (tmm) REVERT: E 34 ARG cc_start: 0.9023 (ttt180) cc_final: 0.8472 (tpp80) REVERT: E 62 GLU cc_start: 0.8516 (pm20) cc_final: 0.7492 (mp0) REVERT: E 66 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7531 (tm-30) REVERT: E 116 TYR cc_start: 0.9357 (m-80) cc_final: 0.9025 (m-80) REVERT: F 13 MET cc_start: 0.8276 (tmm) cc_final: 0.7722 (tmm) REVERT: F 15 LYS cc_start: 0.8744 (mttt) cc_final: 0.8010 (mtpm) REVERT: F 18 ASP cc_start: 0.8926 (m-30) cc_final: 0.8550 (m-30) REVERT: F 30 MET cc_start: 0.8407 (ttm) cc_final: 0.7907 (tmm) REVERT: F 34 ARG cc_start: 0.9003 (ttt180) cc_final: 0.8292 (tpp80) REVERT: F 35 LYS cc_start: 0.9307 (ttpt) cc_final: 0.8927 (ttmm) REVERT: F 62 GLU cc_start: 0.8366 (pm20) cc_final: 0.7548 (pm20) REVERT: F 63 GLU cc_start: 0.7945 (pm20) cc_final: 0.7156 (pm20) REVERT: F 66 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7800 (tm-30) REVERT: F 72 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8401 (mp0) REVERT: F 80 LYS cc_start: 0.8969 (tttt) cc_final: 0.8662 (tttm) REVERT: F 89 GLU cc_start: 0.8122 (mp0) cc_final: 0.7684 (mp0) REVERT: G 13 MET cc_start: 0.8607 (tmm) cc_final: 0.7867 (tmm) REVERT: G 15 LYS cc_start: 0.8959 (mttt) cc_final: 0.8333 (mttp) REVERT: G 21 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8266 (mtp-110) REVERT: G 30 MET cc_start: 0.8505 (tmm) cc_final: 0.7718 (tmm) REVERT: G 34 ARG cc_start: 0.8947 (ttt180) cc_final: 0.8357 (tpp80) REVERT: G 63 GLU cc_start: 0.8529 (pt0) cc_final: 0.7507 (pm20) REVERT: G 66 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7724 (tm-30) REVERT: G 72 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8301 (mp0) REVERT: G 104 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8006 (ttm110) REVERT: H 15 LYS cc_start: 0.8687 (mttt) cc_final: 0.8121 (mtpp) REVERT: H 30 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: H 34 ARG cc_start: 0.8997 (ttt180) cc_final: 0.8346 (tpp80) REVERT: H 62 GLU cc_start: 0.8349 (mp0) cc_final: 0.7796 (mp0) REVERT: H 63 GLU cc_start: 0.8799 (pt0) cc_final: 0.8057 (pm20) REVERT: H 66 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7658 (tm-30) REVERT: H 72 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8477 (mp0) REVERT: H 84 ILE cc_start: 0.9328 (mt) cc_final: 0.8833 (pp) REVERT: I 13 MET cc_start: 0.8139 (tmm) cc_final: 0.7749 (tmm) REVERT: I 18 ASP cc_start: 0.8883 (m-30) cc_final: 0.8495 (m-30) REVERT: I 30 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8227 (tmm) REVERT: I 34 ARG cc_start: 0.8824 (ttt180) cc_final: 0.8467 (tpp80) REVERT: I 80 LYS cc_start: 0.8859 (tttt) cc_final: 0.8487 (tttm) REVERT: I 99 ASP cc_start: 0.8703 (t0) cc_final: 0.8253 (t70) REVERT: I 100 SER cc_start: 0.8766 (t) cc_final: 0.8470 (p) REVERT: I 104 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7792 (ttm110) REVERT: J 13 MET cc_start: 0.8475 (tmm) cc_final: 0.8232 (tmm) REVERT: J 15 LYS cc_start: 0.8656 (mttt) cc_final: 0.7960 (ttmm) REVERT: J 21 ARG cc_start: 0.8392 (mmm160) cc_final: 0.8177 (mmm160) REVERT: J 30 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8200 (mmm) REVERT: J 34 ARG cc_start: 0.8664 (ttt180) cc_final: 0.8327 (ttt-90) REVERT: J 61 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: J 62 GLU cc_start: 0.8387 (mp0) cc_final: 0.8180 (mp0) REVERT: J 63 GLU cc_start: 0.8681 (pt0) cc_final: 0.8417 (pt0) REVERT: J 66 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7576 (tm-30) REVERT: J 84 ILE cc_start: 0.9410 (mt) cc_final: 0.8917 (pp) REVERT: J 89 GLU cc_start: 0.7482 (mp0) cc_final: 0.7233 (mp0) REVERT: J 100 SER cc_start: 0.8944 (t) cc_final: 0.8566 (p) REVERT: K 13 MET cc_start: 0.8226 (tmm) cc_final: 0.7933 (tmm) REVERT: K 15 LYS cc_start: 0.8546 (mttt) cc_final: 0.7944 (mtpm) REVERT: K 21 ARG cc_start: 0.8540 (mmm-85) cc_final: 0.8318 (mtp85) REVERT: K 26 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8928 (mp) REVERT: K 62 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7825 (mp0) REVERT: K 63 GLU cc_start: 0.8798 (pt0) cc_final: 0.8598 (pt0) REVERT: K 66 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8189 (tm-30) REVERT: K 76 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7825 (mptt) REVERT: K 80 LYS cc_start: 0.8887 (tttt) cc_final: 0.8507 (tttm) REVERT: K 99 ASP cc_start: 0.8391 (t0) cc_final: 0.7970 (t70) REVERT: K 118 THR cc_start: 0.9178 (m) cc_final: 0.8670 (p) outliers start: 35 outliers final: 14 residues processed: 371 average time/residue: 1.3587 time to fit residues: 529.5860 Evaluate side-chains 356 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 334 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 30 MET 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 30 MET Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE 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 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.0020 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.072529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.053570 restraints weight = 17284.563| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.75 r_work: 0.3335 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8096 Z= 0.295 Angle : 0.894 12.336 11000 Z= 0.447 Chirality : 0.053 0.174 1287 Planarity : 0.006 0.074 1353 Dihedral : 5.701 25.090 1089 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.80 % Allowed : 31.00 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.003 0.001 HIS E 31 PHE 0.028 0.001 PHE K 64 TYR 0.019 0.002 TYR H 116 ARG 0.018 0.002 ARG F 104 *********************** 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 366 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 342 time to evaluate : 0.951 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: 0.8841 (ttt180) cc_final: 0.8250 (tpp80) REVERT: A 63 GLU cc_start: 0.8919 (pt0) cc_final: 0.7967 (pp20) REVERT: A 66 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 70 LYS cc_start: 0.9109 (tppp) cc_final: 0.8866 (tppp) REVERT: A 84 ILE cc_start: 0.9533 (mt) cc_final: 0.9208 (pp) REVERT: A 90 HIS cc_start: 0.8597 (m90) cc_final: 0.8024 (m90) REVERT: A 92 GLU cc_start: 0.8120 (mp0) cc_final: 0.7748 (mp0) REVERT: A 104 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7422 (mtm-85) REVERT: A 106 THR cc_start: 0.9262 (m) cc_final: 0.8970 (p) REVERT: B 13 MET cc_start: 0.8162 (tmm) cc_final: 0.7710 (tmm) REVERT: B 15 LYS cc_start: 0.8636 (mttt) cc_final: 0.7938 (mtpm) REVERT: B 34 ARG cc_start: 0.8855 (ttt180) cc_final: 0.8274 (tpp80) REVERT: B 61 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 62 GLU cc_start: 0.8072 (mp0) cc_final: 0.7317 (mp0) REVERT: B 63 GLU cc_start: 0.7841 (pm20) cc_final: 0.7403 (pm20) REVERT: B 66 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 80 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8622 (ttpt) REVERT: B 104 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7604 (mtm-85) REVERT: C 15 LYS cc_start: 0.8681 (mttt) cc_final: 0.8186 (mtpm) REVERT: C 18 ASP cc_start: 0.8897 (m-30) cc_final: 0.8364 (m-30) REVERT: C 30 MET cc_start: 0.8489 (ttm) cc_final: 0.8005 (tmm) REVERT: C 35 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8934 (ttmt) REVERT: C 62 GLU cc_start: 0.7907 (mp0) cc_final: 0.7420 (mp0) REVERT: C 63 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: C 84 ILE cc_start: 0.9163 (mm) cc_final: 0.8874 (tp) REVERT: C 90 HIS cc_start: 0.8507 (m90) cc_final: 0.8268 (m90) REVERT: D 13 MET cc_start: 0.8147 (tmm) cc_final: 0.7666 (tmm) REVERT: D 15 LYS cc_start: 0.8644 (mttt) cc_final: 0.8010 (mtpm) REVERT: D 34 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8350 (tpp80) REVERT: D 58 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8595 (tp) REVERT: D 62 GLU cc_start: 0.7880 (mp0) cc_final: 0.7578 (mp0) REVERT: D 66 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 80 LYS cc_start: 0.8970 (tttt) cc_final: 0.8608 (tttp) REVERT: D 104 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8096 (mtm-85) REVERT: D 116 TYR cc_start: 0.9483 (m-80) cc_final: 0.9167 (m-80) REVERT: E 13 MET cc_start: 0.8415 (tmm) cc_final: 0.8048 (tmm) REVERT: E 18 ASP cc_start: 0.8836 (m-30) cc_final: 0.8419 (m-30) REVERT: E 30 MET cc_start: 0.8340 (tmm) cc_final: 0.7590 (tmm) REVERT: E 34 ARG cc_start: 0.9051 (ttt180) cc_final: 0.8439 (tpp80) REVERT: E 62 GLU cc_start: 0.8516 (pm20) cc_final: 0.7397 (mp0) REVERT: E 66 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7581 (tm-30) REVERT: E 89 GLU cc_start: 0.8437 (mp0) cc_final: 0.8209 (mp0) REVERT: E 116 TYR cc_start: 0.9377 (m-80) cc_final: 0.9050 (m-80) REVERT: F 13 MET cc_start: 0.8245 (tmm) cc_final: 0.7643 (tmm) REVERT: F 15 LYS cc_start: 0.8762 (mttt) cc_final: 0.8036 (mtpm) REVERT: F 18 ASP cc_start: 0.8941 (m-30) cc_final: 0.8556 (m-30) REVERT: F 30 MET cc_start: 0.8418 (ttm) cc_final: 0.7884 (tmm) REVERT: F 34 ARG cc_start: 0.9012 (ttt180) cc_final: 0.8294 (tpp80) REVERT: F 35 LYS cc_start: 0.9254 (ttpt) cc_final: 0.8805 (ttmm) REVERT: F 62 GLU cc_start: 0.8335 (pm20) cc_final: 0.7537 (pm20) REVERT: F 63 GLU cc_start: 0.7941 (pm20) cc_final: 0.7148 (pm20) REVERT: F 66 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7838 (tm-30) REVERT: F 72 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8423 (mp0) REVERT: F 80 LYS cc_start: 0.8980 (tttt) cc_final: 0.8682 (tttp) REVERT: F 89 GLU cc_start: 0.7940 (mp0) cc_final: 0.7518 (mp0) REVERT: G 13 MET cc_start: 0.8622 (tmm) cc_final: 0.7938 (tmm) REVERT: G 15 LYS cc_start: 0.8952 (mttt) cc_final: 0.8320 (mttp) REVERT: G 30 MET cc_start: 0.8518 (tmm) cc_final: 0.7749 (tmm) REVERT: G 34 ARG cc_start: 0.8950 (ttt180) cc_final: 0.8329 (tpp80) REVERT: G 62 GLU cc_start: 0.8133 (mp0) cc_final: 0.7923 (mp0) REVERT: G 63 GLU cc_start: 0.8536 (pt0) cc_final: 0.7497 (pm20) REVERT: G 66 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7657 (tm-30) REVERT: G 72 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8313 (mp0) REVERT: H 15 LYS cc_start: 0.8692 (mttt) cc_final: 0.8116 (mtpp) REVERT: H 30 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.7878 (tmm) REVERT: H 34 ARG cc_start: 0.9012 (ttt180) cc_final: 0.8456 (tpp80) REVERT: H 35 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8668 (mttt) REVERT: H 62 GLU cc_start: 0.8360 (mp0) cc_final: 0.7769 (mp0) REVERT: H 63 GLU cc_start: 0.8794 (pt0) cc_final: 0.8125 (pm20) REVERT: H 66 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7767 (tm-30) REVERT: H 72 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8432 (mp0) REVERT: H 84 ILE cc_start: 0.9344 (mt) cc_final: 0.8856 (pp) REVERT: I 13 MET cc_start: 0.8087 (tmm) cc_final: 0.7773 (tmm) REVERT: I 18 ASP cc_start: 0.8891 (m-30) cc_final: 0.8438 (m-30) REVERT: I 30 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8236 (tmm) REVERT: I 34 ARG cc_start: 0.8819 (ttt180) cc_final: 0.8373 (tpp80) REVERT: I 70 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9008 (ttpp) REVERT: I 72 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8336 (mp0) REVERT: I 80 LYS cc_start: 0.8868 (tttt) cc_final: 0.8503 (tttm) REVERT: I 99 ASP cc_start: 0.8760 (t0) cc_final: 0.8305 (t70) REVERT: I 100 SER cc_start: 0.8797 (t) cc_final: 0.8508 (p) REVERT: I 104 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7804 (ttm110) REVERT: J 13 MET cc_start: 0.8500 (tmm) cc_final: 0.8023 (tmm) REVERT: J 15 LYS cc_start: 0.8666 (mttt) cc_final: 0.7855 (mtpp) REVERT: J 21 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8226 (mmm160) REVERT: J 30 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8210 (mmm) REVERT: J 34 ARG cc_start: 0.8660 (ttt180) cc_final: 0.8067 (tpp80) REVERT: J 35 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8237 (mttm) REVERT: J 61 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7854 (mt-10) REVERT: J 63 GLU cc_start: 0.8700 (pt0) cc_final: 0.8399 (pt0) REVERT: J 66 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7750 (tm-30) REVERT: J 84 ILE cc_start: 0.9368 (mt) cc_final: 0.8896 (pp) REVERT: J 100 SER cc_start: 0.8941 (t) cc_final: 0.8564 (p) REVERT: K 13 MET cc_start: 0.8260 (tmm) cc_final: 0.7951 (tmm) REVERT: K 15 LYS cc_start: 0.8579 (mttt) cc_final: 0.8047 (mtpm) REVERT: K 21 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8353 (mtp85) REVERT: K 26 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8908 (mp) REVERT: K 62 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7843 (mp0) REVERT: K 66 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8240 (tm-30) REVERT: K 70 LYS cc_start: 0.9030 (tmtp) cc_final: 0.8767 (tmmm) REVERT: K 76 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7936 (mptt) REVERT: K 80 LYS cc_start: 0.8879 (tttt) cc_final: 0.8487 (tttp) REVERT: K 99 ASP cc_start: 0.8432 (t0) cc_final: 0.8035 (t70) REVERT: K 105 TYR cc_start: 0.8868 (m-80) cc_final: 0.8661 (m-80) REVERT: K 118 THR cc_start: 0.9156 (m) cc_final: 0.8646 (p) outliers start: 24 outliers final: 13 residues processed: 351 average time/residue: 1.3716 time to fit residues: 504.1474 Evaluate side-chains 350 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 330 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 70 LYS Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 26 ILE 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 2 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.070838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.051963 restraints weight = 17333.723| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.66 r_work: 0.3296 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8096 Z= 0.416 Angle : 0.947 12.456 11000 Z= 0.476 Chirality : 0.054 0.194 1287 Planarity : 0.007 0.082 1353 Dihedral : 5.857 25.303 1089 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.91 % Allowed : 30.77 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.24), 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 TRP 0.005 0.001 TRP E 79 HIS 0.002 0.001 HIS A 88 PHE 0.028 0.002 PHE K 64 TYR 0.019 0.002 TYR I 116 ARG 0.019 0.003 ARG F 104 ********************** 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 358 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 0.953 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: 0.8811 (mttt) cc_final: 0.8373 (mtpm) REVERT: A 34 ARG cc_start: 0.8822 (ttt180) cc_final: 0.8227 (tpp80) REVERT: A 62 GLU cc_start: 0.8345 (mp0) cc_final: 0.8059 (mp0) REVERT: A 63 GLU cc_start: 0.8903 (pt0) cc_final: 0.8166 (pp20) REVERT: A 66 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 70 LYS cc_start: 0.9081 (tppp) cc_final: 0.8867 (tppp) REVERT: A 84 ILE cc_start: 0.9519 (mt) cc_final: 0.9195 (pp) REVERT: A 90 HIS cc_start: 0.8488 (m90) cc_final: 0.7839 (m90) REVERT: A 92 GLU cc_start: 0.8173 (mp0) cc_final: 0.7796 (mp0) REVERT: A 104 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7473 (mtm-85) REVERT: A 106 THR cc_start: 0.9246 (m) cc_final: 0.8926 (p) REVERT: B 13 MET cc_start: 0.8138 (tmm) cc_final: 0.7737 (tmm) REVERT: B 15 LYS cc_start: 0.8687 (mttt) cc_final: 0.8029 (mtpm) REVERT: B 21 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7988 (tpp80) REVERT: B 34 ARG cc_start: 0.8847 (ttt180) cc_final: 0.8299 (tpp80) REVERT: B 61 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7742 (mt-10) REVERT: B 62 GLU cc_start: 0.8125 (mp0) cc_final: 0.7368 (mp0) REVERT: B 66 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 80 LYS cc_start: 0.9031 (ttpt) cc_final: 0.8637 (ttpt) REVERT: B 104 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: C 15 LYS cc_start: 0.8711 (mttt) cc_final: 0.8187 (mtpm) REVERT: C 18 ASP cc_start: 0.8932 (m-30) cc_final: 0.8387 (m-30) REVERT: C 30 MET cc_start: 0.8614 (ttm) cc_final: 0.8002 (tmm) REVERT: C 35 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8928 (ttmt) REVERT: C 62 GLU cc_start: 0.7929 (mp0) cc_final: 0.7423 (mp0) REVERT: C 63 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: C 72 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8605 (mm-30) REVERT: C 90 HIS cc_start: 0.8548 (m90) cc_final: 0.8078 (m90) REVERT: C 104 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.8048 (mtm-85) REVERT: D 13 MET cc_start: 0.8174 (tmm) cc_final: 0.7712 (tmm) REVERT: D 15 LYS cc_start: 0.8767 (mttt) cc_final: 0.8115 (mtpm) REVERT: D 34 ARG cc_start: 0.9050 (ttt180) cc_final: 0.8427 (tpp80) REVERT: D 58 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8640 (tp) REVERT: D 61 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 62 GLU cc_start: 0.7948 (mp0) cc_final: 0.7737 (mp0) REVERT: D 63 GLU cc_start: 0.7787 (pm20) cc_final: 0.7541 (pm20) REVERT: D 66 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7844 (tm-30) REVERT: D 80 LYS cc_start: 0.8974 (tttt) cc_final: 0.8612 (tttm) REVERT: D 104 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.7973 (mtm-85) REVERT: D 116 TYR cc_start: 0.9480 (m-80) cc_final: 0.9207 (m-80) REVERT: E 13 MET cc_start: 0.8426 (tmm) cc_final: 0.8036 (tmm) REVERT: E 18 ASP cc_start: 0.8863 (m-30) cc_final: 0.8398 (m-30) REVERT: E 30 MET cc_start: 0.8401 (tmm) cc_final: 0.7648 (tmm) REVERT: E 34 ARG cc_start: 0.9075 (ttt180) cc_final: 0.8449 (tpp80) REVERT: E 62 GLU cc_start: 0.8452 (pm20) cc_final: 0.7739 (pm20) REVERT: E 66 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7631 (tm-30) REVERT: E 89 GLU cc_start: 0.8417 (mp0) cc_final: 0.8161 (mp0) REVERT: E 116 TYR cc_start: 0.9376 (m-80) cc_final: 0.9087 (m-80) REVERT: F 13 MET cc_start: 0.8311 (tmm) cc_final: 0.7735 (tmm) REVERT: F 15 LYS cc_start: 0.8785 (mttt) cc_final: 0.8057 (mtpm) REVERT: F 18 ASP cc_start: 0.8943 (m-30) cc_final: 0.8558 (m-30) REVERT: F 30 MET cc_start: 0.8461 (ttm) cc_final: 0.7887 (tmm) REVERT: F 34 ARG cc_start: 0.9008 (ttt180) cc_final: 0.8295 (tpp80) REVERT: F 35 LYS cc_start: 0.9213 (ttpt) cc_final: 0.8866 (ttmm) REVERT: F 62 GLU cc_start: 0.8417 (pm20) cc_final: 0.7707 (pm20) REVERT: F 63 GLU cc_start: 0.7963 (pm20) cc_final: 0.7165 (pm20) REVERT: F 66 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7905 (tm-30) REVERT: F 80 LYS cc_start: 0.8985 (tttt) cc_final: 0.8684 (tttp) REVERT: F 89 GLU cc_start: 0.7895 (mp0) cc_final: 0.7620 (mp0) REVERT: G 13 MET cc_start: 0.8678 (tmm) cc_final: 0.7921 (tmm) REVERT: G 15 LYS cc_start: 0.8957 (mttt) cc_final: 0.8349 (mttp) REVERT: G 30 MET cc_start: 0.8550 (tmm) cc_final: 0.7679 (tmm) REVERT: G 34 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8317 (tpp80) REVERT: G 62 GLU cc_start: 0.8142 (mp0) cc_final: 0.7883 (mp0) REVERT: G 63 GLU cc_start: 0.8556 (pt0) cc_final: 0.7505 (pm20) REVERT: G 66 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7694 (tm-30) REVERT: G 72 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8299 (mp0) REVERT: G 89 GLU cc_start: 0.8240 (mp0) cc_final: 0.7992 (mp0) REVERT: H 15 LYS cc_start: 0.8703 (mttt) cc_final: 0.8162 (mtpp) REVERT: H 30 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7934 (tmm) REVERT: H 34 ARG cc_start: 0.9040 (ttt180) cc_final: 0.8442 (tpp80) REVERT: H 35 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8607 (mttt) REVERT: H 62 GLU cc_start: 0.8371 (mp0) cc_final: 0.7719 (mp0) REVERT: H 63 GLU cc_start: 0.8782 (pt0) cc_final: 0.8099 (pm20) REVERT: H 66 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7751 (tm-30) REVERT: H 84 ILE cc_start: 0.9378 (mt) cc_final: 0.8894 (pp) REVERT: I 13 MET cc_start: 0.8110 (tmm) cc_final: 0.7730 (tmm) REVERT: I 18 ASP cc_start: 0.8892 (m-30) cc_final: 0.8454 (m-30) REVERT: I 30 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: I 34 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8200 (tpp80) REVERT: I 72 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8602 (mp0) REVERT: I 80 LYS cc_start: 0.8914 (tttt) cc_final: 0.8523 (tttp) REVERT: I 99 ASP cc_start: 0.8824 (t0) cc_final: 0.8352 (t70) REVERT: I 100 SER cc_start: 0.8803 (t) cc_final: 0.8527 (p) REVERT: I 104 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7862 (ttm110) REVERT: J 13 MET cc_start: 0.8474 (tmm) cc_final: 0.8163 (tmm) REVERT: J 15 LYS cc_start: 0.8681 (mttt) cc_final: 0.7949 (ttmm) REVERT: J 21 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8225 (mmm160) REVERT: J 30 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: J 34 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8034 (tpp80) REVERT: J 35 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8370 (mttm) REVERT: J 62 GLU cc_start: 0.8288 (mp0) cc_final: 0.8062 (mp0) REVERT: J 63 GLU cc_start: 0.8758 (pt0) cc_final: 0.8427 (pt0) REVERT: J 66 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7706 (tm-30) REVERT: J 84 ILE cc_start: 0.9368 (mt) cc_final: 0.8898 (pp) REVERT: J 100 SER cc_start: 0.8941 (t) cc_final: 0.8584 (p) REVERT: K 13 MET cc_start: 0.8207 (tmm) cc_final: 0.7923 (tmm) REVERT: K 15 LYS cc_start: 0.8544 (mttt) cc_final: 0.7938 (mtpm) REVERT: K 21 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8360 (mtp85) REVERT: K 26 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8929 (mp) REVERT: K 62 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7897 (mp0) REVERT: K 66 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8210 (tm-30) REVERT: K 70 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8801 (tmmm) REVERT: K 73 ILE cc_start: 0.8261 (mt) cc_final: 0.7895 (mp) REVERT: K 76 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7898 (mptt) REVERT: K 80 LYS cc_start: 0.8889 (tttt) cc_final: 0.8498 (tttm) REVERT: K 99 ASP cc_start: 0.8500 (t0) cc_final: 0.8062 (t70) outliers start: 25 outliers final: 13 residues processed: 344 average time/residue: 1.6345 time to fit residues: 588.1421 Evaluate side-chains 346 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 326 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 58 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 30 MET Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain K residue 26 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 62 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.073827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054641 restraints weight = 17014.088| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.71 r_work: 0.3372 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8096 Z= 0.297 Angle : 0.925 14.039 11000 Z= 0.461 Chirality : 0.053 0.176 1287 Planarity : 0.007 0.084 1353 Dihedral : 5.770 24.493 1089 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.21 % Allowed : 31.70 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.24), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.007 0.001 HIS B 90 PHE 0.028 0.001 PHE K 64 TYR 0.028 0.002 TYR K 105 ARG 0.021 0.002 ARG K 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8924.63 seconds wall clock time: 158 minutes 0.69 seconds (9480.69 seconds total)