Starting phenix.real_space_refine on Wed Feb 12 10:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sdz_10150/02_2025/6sdz_10150.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sdz_10150/02_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_10150/02_2025/6sdz_10150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sdz_10150/02_2025/6sdz_10150.map" model { file = "/net/cci-nas-00/data/ceres_data/6sdz_10150/02_2025/6sdz_10150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sdz_10150/02_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-5592/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: 4.88, per 1000 atoms: 0.62 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: 1.79 Conformation dependent library (CDL) restraints added in 1.0 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: 1.28 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: 2.29 Time building geometry restraints manager: 2.10 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: 0.340 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.880 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- 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 : 0.923 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: 1.3036 time to fit residues: 538.9765 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 : 0.974 ------------------------------------------------------------------------------- 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 = 0.074981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.056228 restraints weight = 16730.384| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.65 r_work: 0.3409 rms_B_bonded: 3.56 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 8.876 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 : 0.862 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: 0.8255 (tmm) REVERT: A 15 LYS cc_start: 0.8915 (mttt) cc_final: 0.8246 (mtpm) REVERT: A 18 ASP cc_start: 0.8525 (m-30) cc_final: 0.8291 (m-30) REVERT: A 34 ARG cc_start: 0.8680 (ttt180) cc_final: 0.7955 (tpp80) REVERT: A 63 GLU cc_start: 0.8869 (pt0) cc_final: 0.8227 (pp20) REVERT: A 66 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 88 HIS cc_start: 0.9255 (t-90) cc_final: 0.8986 (t-90) REVERT: A 89 GLU cc_start: 0.7482 (mp0) cc_final: 0.7142 (pm20) REVERT: A 90 HIS cc_start: 0.8326 (m90) cc_final: 0.7968 (m90) REVERT: A 104 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7905 (mtt-85) REVERT: A 106 THR cc_start: 0.9261 (m) cc_final: 0.8932 (p) REVERT: B 13 MET cc_start: 0.7947 (tmm) cc_final: 0.7559 (tmm) REVERT: B 15 LYS cc_start: 0.8656 (mttt) cc_final: 0.8169 (mtpp) REVERT: B 21 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7893 (tpp80) REVERT: B 34 ARG cc_start: 0.8658 (ttt180) cc_final: 0.8080 (tpp80) REVERT: B 62 GLU cc_start: 0.7980 (mp0) cc_final: 0.7663 (mp0) REVERT: B 66 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 80 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8627 (ttpt) REVERT: B 90 HIS cc_start: 0.8196 (m90) cc_final: 0.7809 (m90) REVERT: B 92 GLU cc_start: 0.7057 (mp0) cc_final: 0.6730 (mp0) REVERT: B 99 ASP cc_start: 0.9013 (t70) cc_final: 0.8790 (t70) REVERT: B 104 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7943 (ttm110) REVERT: C 30 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: C 63 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: C 66 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7611 (tm-30) REVERT: C 90 HIS cc_start: 0.8316 (m90) cc_final: 0.8069 (m90) REVERT: D 13 MET cc_start: 0.7989 (tmm) cc_final: 0.7265 (tmm) REVERT: D 15 LYS cc_start: 0.8417 (mttt) cc_final: 0.7771 (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: 0.8415 (tpp80) REVERT: D 63 GLU cc_start: 0.7871 (pm20) cc_final: 0.7611 (pm20) REVERT: D 66 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7835 (tm-30) REVERT: D 69 TYR cc_start: 0.8482 (m-80) cc_final: 0.8087 (m-80) REVERT: D 80 LYS cc_start: 0.8886 (tttt) cc_final: 0.8560 (tttp) REVERT: D 99 ASP cc_start: 0.8962 (t70) cc_final: 0.8740 (t70) REVERT: D 104 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8367 (mtm-85) REVERT: D 116 TYR cc_start: 0.9456 (m-80) cc_final: 0.9120 (m-80) REVERT: E 13 MET cc_start: 0.8196 (tmm) cc_final: 0.7349 (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: 0.9117 (mt) cc_final: 0.8862 (mp) REVERT: E 30 MET cc_start: 0.7389 (tmm) cc_final: 0.7022 (tmm) REVERT: E 34 ARG cc_start: 0.8921 (ttt180) cc_final: 0.8351 (tpp80) REVERT: E 62 GLU cc_start: 0.8113 (pm20) cc_final: 0.7909 (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: 0.8639 (ttm110) cc_final: 0.8034 (mtm-85) REVERT: E 116 TYR cc_start: 0.9340 (m-80) cc_final: 0.9044 (m-80) REVERT: F 13 MET cc_start: 0.7767 (tmm) cc_final: 0.7051 (tmm) REVERT: F 15 LYS cc_start: 0.8539 (mttt) cc_final: 0.7957 (mtpm) REVERT: F 21 ARG cc_start: 0.8566 (tpt-90) cc_final: 0.8158 (mmm160) REVERT: F 30 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7923 (tmm) REVERT: F 34 ARG cc_start: 0.8936 (ttt180) cc_final: 0.8428 (tpp80) REVERT: F 63 GLU cc_start: 0.7872 (pm20) cc_final: 0.7097 (pm20) REVERT: F 66 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 72 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8583 (mt-10) REVERT: F 80 LYS cc_start: 0.8912 (tttt) cc_final: 0.8612 (tttm) REVERT: F 89 GLU cc_start: 0.7818 (mp0) cc_final: 0.7589 (mp0) REVERT: G 13 MET cc_start: 0.8238 (tmm) cc_final: 0.7700 (tmm) REVERT: G 15 LYS cc_start: 0.8751 (mttt) cc_final: 0.8250 (mttm) REVERT: G 34 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8214 (tpp80) REVERT: G 63 GLU cc_start: 0.8517 (pt0) cc_final: 0.7660 (pm20) REVERT: G 66 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 104 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8069 (ttm110) REVERT: H 15 LYS cc_start: 0.8550 (mttt) cc_final: 0.8034 (mtpp) REVERT: H 34 ARG cc_start: 0.9025 (ttt180) cc_final: 0.8407 (tpp80) REVERT: H 62 GLU cc_start: 0.7839 (mp0) cc_final: 0.7478 (mp0) REVERT: H 63 GLU cc_start: 0.8633 (pt0) cc_final: 0.7885 (pm20) REVERT: H 66 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7630 (tm-30) REVERT: I 13 MET cc_start: 0.7991 (tmm) cc_final: 0.7746 (tmm) REVERT: I 15 LYS cc_start: 0.8549 (mttt) cc_final: 0.7964 (mtpp) REVERT: I 34 ARG cc_start: 0.8753 (ttt180) cc_final: 0.8429 (tpp80) REVERT: I 62 GLU cc_start: 0.8023 (mp0) cc_final: 0.7705 (mp0) REVERT: I 63 GLU cc_start: 0.8472 (pt0) cc_final: 0.8249 (pt0) REVERT: I 80 LYS cc_start: 0.8845 (tttt) cc_final: 0.8497 (tttp) REVERT: I 89 GLU cc_start: 0.7946 (mp0) cc_final: 0.7699 (pm20) REVERT: I 99 ASP cc_start: 0.8863 (t0) cc_final: 0.8354 (t70) REVERT: I 100 SER cc_start: 0.8698 (t) cc_final: 0.8388 (p) REVERT: I 104 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7740 (ttm110) REVERT: J 13 MET cc_start: 0.8255 (tmm) cc_final: 0.7714 (tmm) REVERT: J 15 LYS cc_start: 0.8514 (mttt) cc_final: 0.7881 (ttmm) REVERT: J 21 ARG cc_start: 0.8355 (mmm160) cc_final: 0.8077 (mmm160) REVERT: J 34 ARG cc_start: 0.8521 (ttt180) cc_final: 0.7802 (tpp80) REVERT: J 35 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8715 (ttmm) REVERT: J 62 GLU cc_start: 0.8132 (mp0) cc_final: 0.7844 (mp0) REVERT: J 63 GLU cc_start: 0.8495 (pt0) cc_final: 0.8057 (pt0) REVERT: J 66 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7789 (tm-30) REVERT: J 72 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (mm-30) REVERT: J 84 ILE cc_start: 0.9336 (mt) cc_final: 0.8765 (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: 0.8567 (p) REVERT: K 15 LYS cc_start: 0.8540 (mttt) cc_final: 0.7960 (mtpm) REVERT: K 21 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.8200 (mtp85) REVERT: K 30 MET cc_start: 0.7945 (ppp) cc_final: 0.7698 (ppp) REVERT: K 35 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8768 (ttmt) REVERT: K 62 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7784 (mp0) REVERT: K 63 GLU cc_start: 0.8691 (pt0) cc_final: 0.8389 (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: 0.8708 (m90) cc_final: 0.8445 (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: 0.8643 (p) REVERT: K 118 THR cc_start: 0.9214 (m) cc_final: 0.8876 (p) outliers start: 36 outliers final: 6 residues processed: 381 average time/residue: 1.3778 time to fit residues: 550.8615 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 : 0.946 ------------------------------------------------------------------------------- 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: 2.9990 chunk 75 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.069364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049813 restraints weight = 17962.219| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.72 r_work: 0.3143 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 8096 Z= 0.504 Angle : 0.788 9.007 11000 Z= 0.413 Chirality : 0.053 0.147 1287 Planarity : 0.005 0.045 1353 Dihedral : 5.988 24.808 1089 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.31 % Allowed : 22.14 % Favored : 73.54 % 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 0.019 0.003 TYR K 105 ARG 0.011 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 375 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 0.754 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: 0.8653 (ttt180) cc_final: 0.8119 (tpp80) REVERT: A 63 GLU cc_start: 0.8865 (pt0) cc_final: 0.8243 (pp20) REVERT: A 66 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 70 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8710 (tppp) REVERT: A 90 HIS cc_start: 0.8243 (m90) cc_final: 0.8011 (m90) REVERT: A 104 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7220 (mtm-85) REVERT: B 13 MET cc_start: 0.7918 (tmm) cc_final: 0.7548 (tmm) REVERT: B 15 LYS cc_start: 0.8577 (mttt) cc_final: 0.7895 (mtpm) REVERT: B 21 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7895 (tpp80) REVERT: B 34 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8141 (tpp80) REVERT: B 61 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 62 GLU cc_start: 0.7865 (mp0) cc_final: 0.7575 (mp0) REVERT: B 66 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 80 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8646 (ttpt) REVERT: B 90 HIS cc_start: 0.8231 (m90) cc_final: 0.7827 (m90) REVERT: B 99 ASP cc_start: 0.9003 (t70) cc_final: 0.8788 (t70) REVERT: B 104 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: C 15 LYS cc_start: 0.8647 (mttt) cc_final: 0.8094 (mtpm) REVERT: C 63 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7360 (pm20) REVERT: C 66 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: C 90 HIS cc_start: 0.8406 (m90) cc_final: 0.8170 (m90) REVERT: D 13 MET cc_start: 0.8050 (tmm) cc_final: 0.7655 (tmm) REVERT: D 34 ARG cc_start: 0.9038 (ttt180) cc_final: 0.8509 (tpp80) REVERT: D 62 GLU cc_start: 0.7895 (mp0) cc_final: 0.7636 (mp0) REVERT: D 66 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7911 (tm-30) REVERT: D 80 LYS cc_start: 0.8952 (tttt) cc_final: 0.8613 (tttm) REVERT: E 13 MET cc_start: 0.8338 (tmm) cc_final: 0.7998 (tmm) REVERT: E 21 ARG cc_start: 0.8462 (tpt-90) cc_final: 0.7977 (mmm160) REVERT: E 26 ILE cc_start: 0.9152 (mt) cc_final: 0.8893 (mp) REVERT: E 30 MET cc_start: 0.7713 (tmm) cc_final: 0.6874 (tmm) REVERT: E 34 ARG cc_start: 0.8937 (ttt180) cc_final: 0.8400 (tpp80) REVERT: E 62 GLU cc_start: 0.8362 (pm20) cc_final: 0.7962 (pm20) REVERT: E 66 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7888 (tm-30) REVERT: E 116 TYR cc_start: 0.9381 (m-80) cc_final: 0.9157 (m-80) REVERT: F 13 MET cc_start: 0.8075 (tmm) cc_final: 0.7477 (tmm) REVERT: F 15 LYS cc_start: 0.8750 (mttt) cc_final: 0.8238 (mtpm) REVERT: F 18 ASP cc_start: 0.8971 (m-30) cc_final: 0.8703 (m-30) REVERT: F 30 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7995 (tmm) REVERT: F 34 ARG cc_start: 0.8975 (ttt180) cc_final: 0.8266 (tpp80) REVERT: F 35 LYS cc_start: 0.9118 (ttpt) cc_final: 0.8806 (ttmm) REVERT: F 62 GLU cc_start: 0.8090 (pm20) cc_final: 0.7856 (pm20) REVERT: F 63 GLU cc_start: 0.7911 (pm20) cc_final: 0.7215 (pm20) REVERT: F 66 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7690 (tm-30) REVERT: F 72 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8637 (mt-10) REVERT: F 80 LYS cc_start: 0.8963 (tttt) cc_final: 0.8649 (tttp) REVERT: F 84 ILE cc_start: 0.9304 (mm) cc_final: 0.8854 (pp) REVERT: F 89 GLU cc_start: 0.7746 (mp0) cc_final: 0.7359 (mp0) REVERT: G 13 MET cc_start: 0.8570 (tmm) cc_final: 0.8275 (tmm) REVERT: G 34 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8246 (tpp80) REVERT: G 61 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7902 (mt-10) REVERT: G 63 GLU cc_start: 0.8509 (pt0) cc_final: 0.7663 (pm20) REVERT: G 66 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7663 (tm-30) REVERT: G 70 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8984 (ttpp) REVERT: G 72 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8165 (mp0) REVERT: G 104 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8152 (ttm110) REVERT: H 15 LYS cc_start: 0.8629 (mttt) cc_final: 0.8276 (mtpt) REVERT: H 34 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8354 (tpp80) REVERT: H 62 GLU cc_start: 0.8149 (mp0) cc_final: 0.7510 (mp0) REVERT: H 63 GLU cc_start: 0.8740 (pt0) cc_final: 0.7980 (pm20) REVERT: H 66 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7871 (tm-30) REVERT: I 13 MET cc_start: 0.8073 (tmm) cc_final: 0.7679 (tmm) REVERT: I 15 LYS cc_start: 0.8783 (mttt) cc_final: 0.8217 (mtpp) REVERT: I 30 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7932 (mtp) REVERT: I 34 ARG cc_start: 0.8741 (ttt180) cc_final: 0.8349 (tpp80) REVERT: I 70 LYS cc_start: 0.9349 (ttmm) cc_final: 0.8971 (ttpp) REVERT: I 80 LYS cc_start: 0.8892 (tttt) cc_final: 0.8540 (tttp) REVERT: I 100 SER cc_start: 0.8763 (t) cc_final: 0.8445 (p) REVERT: I 104 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7902 (ttm110) REVERT: J 13 MET cc_start: 0.8437 (tmm) cc_final: 0.8048 (tmm) REVERT: J 21 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8201 (mmm160) REVERT: J 34 ARG cc_start: 0.8592 (ttt180) cc_final: 0.7904 (tpp80) REVERT: J 63 GLU cc_start: 0.8544 (pt0) cc_final: 0.8184 (pt0) REVERT: J 66 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7608 (tm-30) REVERT: J 84 ILE cc_start: 0.9284 (mt) cc_final: 0.8745 (pp) REVERT: J 89 GLU cc_start: 0.7796 (mp0) cc_final: 0.7576 (mp0) REVERT: J 100 SER cc_start: 0.8992 (t) cc_final: 0.8662 (p) REVERT: K 13 MET cc_start: 0.8170 (tmm) cc_final: 0.7654 (tmt) REVERT: K 15 LYS cc_start: 0.8492 (mttt) cc_final: 0.7897 (mtpm) REVERT: K 21 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8215 (mtp85) REVERT: K 62 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7640 (mp0) REVERT: K 63 GLU cc_start: 0.8705 (pt0) cc_final: 0.8437 (pt0) REVERT: K 66 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8316 (tm-30) REVERT: K 80 LYS cc_start: 0.8929 (tttt) cc_final: 0.8515 (tttm) REVERT: K 90 HIS cc_start: 0.8660 (m90) cc_final: 0.8324 (m90) REVERT: K 99 ASP cc_start: 0.8486 (t0) cc_final: 0.8211 (t70) REVERT: K 100 SER cc_start: 0.8947 (t) cc_final: 0.8689 (p) REVERT: K 118 THR cc_start: 0.9184 (m) cc_final: 0.8798 (p) outliers start: 37 outliers final: 14 residues processed: 353 average time/residue: 1.4409 time to fit residues: 532.1806 Evaluate side-chains 339 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 319 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.072692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.053220 restraints weight = 16931.756| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.67 r_work: 0.3325 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8096 Z= 0.240 Angle : 0.752 9.458 11000 Z= 0.382 Chirality : 0.051 0.151 1287 Planarity : 0.005 0.049 1353 Dihedral : 5.721 22.639 1089 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.01 % Allowed : 23.19 % Favored : 71.79 % 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 : -2.10 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.004 0.001 HIS C 88 PHE 0.029 0.001 PHE K 64 TYR 0.023 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 399 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 356 time to evaluate : 0.938 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: 0.8746 (ttt180) cc_final: 0.8084 (tpp80) REVERT: A 62 GLU cc_start: 0.7862 (mp0) cc_final: 0.7508 (mp0) REVERT: A 63 GLU cc_start: 0.8880 (pt0) cc_final: 0.8186 (pp20) REVERT: A 66 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 70 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8856 (tppp) REVERT: A 89 GLU cc_start: 0.7724 (pm20) cc_final: 0.6454 (pm20) REVERT: A 90 HIS cc_start: 0.8408 (m90) cc_final: 0.7958 (m90) REVERT: A 92 GLU cc_start: 0.7718 (mp0) cc_final: 0.7499 (mp0) REVERT: A 104 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: A 106 THR cc_start: 0.9197 (m) cc_final: 0.8835 (t) REVERT: B 13 MET cc_start: 0.8046 (tmm) cc_final: 0.7755 (tmm) REVERT: B 15 LYS cc_start: 0.8653 (mttt) cc_final: 0.7933 (mtpm) REVERT: B 30 MET cc_start: 0.7664 (tmm) cc_final: 0.7045 (tmm) REVERT: B 34 ARG cc_start: 0.8768 (ttt180) cc_final: 0.8057 (tpp80) REVERT: B 35 LYS cc_start: 0.9101 (ttmt) cc_final: 0.8867 (mtpp) REVERT: B 61 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7833 (mt-10) REVERT: B 62 GLU cc_start: 0.7859 (mp0) cc_final: 0.7112 (mp0) REVERT: B 63 GLU cc_start: 0.7831 (pm20) cc_final: 0.7629 (pm20) REVERT: B 66 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7461 (tm-30) REVERT: B 69 TYR cc_start: 0.9371 (m-80) cc_final: 0.9149 (m-80) REVERT: B 80 LYS cc_start: 0.9014 (ttpt) cc_final: 0.8647 (ttpt) REVERT: B 90 HIS cc_start: 0.8292 (m90) cc_final: 0.7886 (m90) REVERT: B 92 GLU cc_start: 0.7258 (mp0) cc_final: 0.7044 (mp0) REVERT: B 104 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7395 (mtm-85) REVERT: C 15 LYS cc_start: 0.8654 (mttt) cc_final: 0.8107 (mtpm) REVERT: C 18 ASP cc_start: 0.8864 (m-30) cc_final: 0.8335 (m-30) REVERT: C 30 MET cc_start: 0.8391 (ttm) cc_final: 0.8009 (tmm) REVERT: C 62 GLU cc_start: 0.7966 (mp0) cc_final: 0.7579 (mp0) REVERT: C 63 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: C 66 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8068 (pp20) REVERT: C 90 HIS cc_start: 0.8547 (m90) cc_final: 0.8251 (m90) REVERT: D 13 MET cc_start: 0.8050 (tmm) cc_final: 0.7513 (tmm) REVERT: D 15 LYS cc_start: 0.8565 (mttt) cc_final: 0.7940 (mtpm) REVERT: D 34 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8480 (tpp80) REVERT: D 62 GLU cc_start: 0.7862 (mp0) cc_final: 0.7508 (mp0) REVERT: D 63 GLU cc_start: 0.7867 (pm20) cc_final: 0.7652 (pm20) REVERT: D 66 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7679 (tm-30) REVERT: D 80 LYS cc_start: 0.8966 (tttt) cc_final: 0.8606 (tttp) REVERT: D 104 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8149 (ttm110) REVERT: D 116 TYR cc_start: 0.9460 (m-80) cc_final: 0.9247 (m-80) REVERT: E 13 MET cc_start: 0.8347 (tmm) cc_final: 0.8047 (tmm) REVERT: E 30 MET cc_start: 0.7905 (tmm) cc_final: 0.7434 (tmm) REVERT: E 34 ARG cc_start: 0.8961 (ttt180) cc_final: 0.8422 (tpp80) REVERT: E 35 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8842 (mtpt) REVERT: E 62 GLU cc_start: 0.8382 (pm20) cc_final: 0.7922 (pm20) REVERT: E 66 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7727 (tm-30) REVERT: E 72 GLU cc_start: 0.8928 (mt-10) cc_final: 0.7478 (mp0) REVERT: F 13 MET cc_start: 0.8122 (tmm) cc_final: 0.7653 (tmm) REVERT: F 15 LYS cc_start: 0.8730 (mttt) cc_final: 0.8076 (mtpm) REVERT: F 18 ASP cc_start: 0.8888 (m-30) cc_final: 0.8599 (m-30) REVERT: F 30 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7884 (tmm) REVERT: F 34 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8258 (tpp80) REVERT: F 35 LYS cc_start: 0.9194 (ttpt) cc_final: 0.8816 (ttmm) REVERT: F 62 GLU cc_start: 0.8190 (pm20) cc_final: 0.7916 (pm20) REVERT: F 63 GLU cc_start: 0.7894 (pm20) cc_final: 0.7263 (pm20) REVERT: F 66 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 69 TYR cc_start: 0.9280 (m-80) cc_final: 0.9023 (m-80) REVERT: F 70 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8979 (ptmm) REVERT: F 80 LYS cc_start: 0.8940 (tttt) cc_final: 0.8623 (tttm) REVERT: F 84 ILE cc_start: 0.9428 (mm) cc_final: 0.8970 (pp) REVERT: F 89 GLU cc_start: 0.7923 (mp0) cc_final: 0.7439 (mp0) REVERT: G 13 MET cc_start: 0.8604 (tmm) cc_final: 0.7821 (tmm) REVERT: G 15 LYS cc_start: 0.8947 (mttt) cc_final: 0.8247 (mttm) REVERT: G 30 MET cc_start: 0.7943 (tmm) cc_final: 0.7632 (tmm) REVERT: G 34 ARG cc_start: 0.8874 (ttt180) cc_final: 0.8274 (tpp80) REVERT: G 61 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7956 (mt-10) REVERT: G 63 GLU cc_start: 0.8519 (pt0) cc_final: 0.7544 (pm20) REVERT: G 66 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7590 (tm-30) REVERT: G 104 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8086 (ttm110) REVERT: H 15 LYS cc_start: 0.8612 (mttt) cc_final: 0.8042 (mtpm) REVERT: H 34 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8314 (tpp80) REVERT: H 62 GLU cc_start: 0.8201 (mp0) cc_final: 0.7588 (mp0) REVERT: H 63 GLU cc_start: 0.8704 (pt0) cc_final: 0.7964 (pm20) REVERT: H 66 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7640 (tm-30) REVERT: I 13 MET cc_start: 0.7999 (tmm) cc_final: 0.7649 (tmm) REVERT: I 15 LYS cc_start: 0.8703 (mttt) cc_final: 0.8034 (mtpp) REVERT: I 30 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7736 (mtp) REVERT: I 34 ARG cc_start: 0.8768 (ttt180) cc_final: 0.8399 (tpp80) REVERT: I 70 LYS cc_start: 0.9333 (ttmm) cc_final: 0.9042 (ttpp) REVERT: I 80 LYS cc_start: 0.8868 (tttt) cc_final: 0.8504 (tttm) REVERT: I 99 ASP cc_start: 0.8715 (t0) cc_final: 0.8195 (t70) REVERT: I 100 SER cc_start: 0.8771 (t) cc_final: 0.8457 (p) REVERT: I 104 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7792 (ttm110) REVERT: J 13 MET cc_start: 0.8506 (tmm) cc_final: 0.8147 (tmm) REVERT: J 15 LYS cc_start: 0.8576 (mttt) cc_final: 0.7840 (ttmm) REVERT: J 21 ARG cc_start: 0.8343 (mmm160) cc_final: 0.8129 (mmm160) REVERT: J 34 ARG cc_start: 0.8612 (ttt180) cc_final: 0.7924 (tpp80) REVERT: J 35 LYS cc_start: 0.9029 (tppp) cc_final: 0.8828 (ttmm) REVERT: J 62 GLU cc_start: 0.8433 (mp0) cc_final: 0.8172 (mp0) REVERT: J 63 GLU cc_start: 0.8543 (pt0) cc_final: 0.8311 (pt0) REVERT: J 66 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7651 (tm-30) REVERT: J 84 ILE cc_start: 0.9342 (mt) cc_final: 0.8820 (pp) REVERT: J 89 GLU cc_start: 0.7929 (mp0) cc_final: 0.7645 (mp0) REVERT: J 100 SER cc_start: 0.8904 (t) cc_final: 0.8502 (p) REVERT: K 13 MET cc_start: 0.8124 (tmm) cc_final: 0.7842 (tmm) REVERT: K 15 LYS cc_start: 0.8508 (mttt) cc_final: 0.7933 (mtpm) REVERT: K 21 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8272 (mtp85) REVERT: K 62 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7840 (mp0) REVERT: K 63 GLU cc_start: 0.8774 (pt0) cc_final: 0.8554 (pt0) REVERT: K 66 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8276 (tm-30) REVERT: K 80 LYS cc_start: 0.8889 (tttt) cc_final: 0.8493 (tttm) REVERT: K 90 HIS cc_start: 0.8836 (m90) cc_final: 0.8613 (m90) REVERT: K 99 ASP cc_start: 0.8451 (t0) cc_final: 0.8169 (t70) REVERT: K 118 THR cc_start: 0.9224 (m) cc_final: 0.8921 (p) outliers start: 43 outliers final: 17 residues processed: 372 average time/residue: 1.3831 time to fit residues: 539.9884 Evaluate side-chains 358 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 335 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 D residue 30 MET Chi-restraints excluded: chain E residue 58 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 K residue 30 MET Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 1 optimal weight: 0.0050 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 3.1600 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.070364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.050581 restraints weight = 17504.865| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.62 r_work: 0.3169 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8096 Z= 0.424 Angle : 0.796 9.849 11000 Z= 0.405 Chirality : 0.053 0.209 1287 Planarity : 0.005 0.044 1353 Dihedral : 5.780 24.976 1089 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.18 % Allowed : 22.96 % Favored : 70.86 % 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 0.004 0.001 HIS C 88 PHE 0.025 0.002 PHE K 64 TYR 0.022 0.002 TYR A 105 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 384 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 331 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8142 (tpp80) REVERT: A 63 GLU cc_start: 0.8878 (pt0) cc_final: 0.8198 (pp20) REVERT: A 66 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 70 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8754 (tppp) REVERT: A 89 GLU cc_start: 0.7975 (pm20) cc_final: 0.7626 (pm20) REVERT: A 90 HIS cc_start: 0.8354 (m90) cc_final: 0.7928 (m90) REVERT: A 104 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7695 (mtt90) REVERT: A 106 THR cc_start: 0.9125 (m) cc_final: 0.8705 (t) REVERT: B 13 MET cc_start: 0.8015 (tmm) cc_final: 0.7618 (tmm) REVERT: B 15 LYS cc_start: 0.8608 (mttt) cc_final: 0.7861 (mtpm) REVERT: B 21 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8015 (tpp80) REVERT: B 30 MET cc_start: 0.7979 (tmm) cc_final: 0.7727 (tmm) REVERT: B 34 ARG cc_start: 0.8749 (ttt180) cc_final: 0.8140 (tpp80) REVERT: B 35 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8809 (mtpp) REVERT: B 61 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 62 GLU cc_start: 0.7775 (mp0) cc_final: 0.7401 (mp0) REVERT: B 66 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 69 TYR cc_start: 0.9415 (m-80) cc_final: 0.9183 (m-80) REVERT: B 80 LYS cc_start: 0.8990 (ttpt) cc_final: 0.8632 (ttpt) REVERT: B 90 HIS cc_start: 0.8324 (m90) cc_final: 0.7908 (m90) REVERT: C 15 LYS cc_start: 0.8607 (mttt) cc_final: 0.8105 (mtpm) REVERT: C 18 ASP cc_start: 0.8944 (m-30) cc_final: 0.8563 (m-30) REVERT: C 30 MET cc_start: 0.8539 (ttm) cc_final: 0.7731 (tmm) REVERT: C 35 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8873 (ttmm) REVERT: C 62 GLU cc_start: 0.7957 (mp0) cc_final: 0.7576 (mp0) REVERT: C 63 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: C 66 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: C 90 HIS cc_start: 0.8560 (m90) cc_final: 0.8192 (m90) REVERT: D 13 MET cc_start: 0.8079 (tmm) cc_final: 0.7642 (tmm) REVERT: D 15 LYS cc_start: 0.8615 (mttt) cc_final: 0.8068 (mtpm) REVERT: D 34 ARG cc_start: 0.9001 (ttt180) cc_final: 0.8454 (tpp80) REVERT: D 62 GLU cc_start: 0.7853 (mp0) cc_final: 0.7554 (mp0) REVERT: D 66 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7828 (tm-30) REVERT: D 80 LYS cc_start: 0.8967 (tttt) cc_final: 0.8610 (tttm) REVERT: D 104 ARG cc_start: 0.8497 (mtm-85) cc_final: 0.8227 (mtm-85) REVERT: E 13 MET cc_start: 0.8305 (tmm) cc_final: 0.7982 (tmm) REVERT: E 30 MET cc_start: 0.8111 (tmm) cc_final: 0.7491 (tmm) REVERT: E 34 ARG cc_start: 0.8956 (ttt180) cc_final: 0.8360 (tpp80) REVERT: E 62 GLU cc_start: 0.8419 (pm20) cc_final: 0.7399 (mp0) REVERT: E 66 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7740 (tm-30) REVERT: E 72 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8134 (mp0) REVERT: E 116 TYR cc_start: 0.9381 (m-80) cc_final: 0.9133 (m-80) REVERT: F 13 MET cc_start: 0.8139 (tmm) cc_final: 0.7709 (tmm) REVERT: F 15 LYS cc_start: 0.8701 (mttt) cc_final: 0.8036 (mtpm) REVERT: F 18 ASP cc_start: 0.8925 (m-30) cc_final: 0.8579 (m-30) REVERT: F 30 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7867 (tmm) REVERT: F 34 ARG cc_start: 0.8964 (ttt180) cc_final: 0.8257 (tpp80) REVERT: F 35 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8818 (ttmm) REVERT: F 62 GLU cc_start: 0.8186 (pm20) cc_final: 0.7776 (pm20) REVERT: F 63 GLU cc_start: 0.7931 (pm20) cc_final: 0.7247 (pm20) REVERT: F 66 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7610 (tm-30) REVERT: F 80 LYS cc_start: 0.8940 (tttt) cc_final: 0.8619 (tttp) REVERT: F 89 GLU cc_start: 0.7768 (mp0) cc_final: 0.7413 (mp0) REVERT: G 13 MET cc_start: 0.8640 (tmm) cc_final: 0.7906 (tmm) REVERT: G 15 LYS cc_start: 0.8945 (mttt) cc_final: 0.8239 (mttp) REVERT: G 30 MET cc_start: 0.8218 (tmm) cc_final: 0.7338 (tmm) REVERT: G 34 ARG cc_start: 0.8860 (ttt180) cc_final: 0.8245 (tpp80) REVERT: G 63 GLU cc_start: 0.8535 (pt0) cc_final: 0.7583 (pm20) REVERT: G 66 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7547 (tm-30) REVERT: G 70 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8917 (ttpp) REVERT: G 72 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8102 (mp0) REVERT: G 104 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8046 (ttm110) REVERT: H 15 LYS cc_start: 0.8605 (mttt) cc_final: 0.8159 (mtmt) REVERT: H 30 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: H 34 ARG cc_start: 0.8947 (ttt180) cc_final: 0.8320 (tpp80) REVERT: H 62 GLU cc_start: 0.8232 (mp0) cc_final: 0.7517 (mp0) REVERT: H 63 GLU cc_start: 0.8736 (pt0) cc_final: 0.7990 (pm20) REVERT: H 66 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7460 (tm-30) REVERT: H 70 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8996 (ttpp) REVERT: H 84 ILE cc_start: 0.9342 (mt) cc_final: 0.8848 (pp) REVERT: I 13 MET cc_start: 0.8070 (tmm) cc_final: 0.7659 (tmm) REVERT: I 15 LYS cc_start: 0.8735 (mttt) cc_final: 0.8086 (mtpp) REVERT: I 30 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: I 34 ARG cc_start: 0.8733 (ttt180) cc_final: 0.8330 (tpp80) REVERT: I 80 LYS cc_start: 0.8875 (tttt) cc_final: 0.8512 (tttm) REVERT: I 99 ASP cc_start: 0.8848 (t0) cc_final: 0.8300 (t70) REVERT: I 100 SER cc_start: 0.8753 (t) cc_final: 0.8489 (p) REVERT: I 104 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7837 (ttm110) REVERT: J 13 MET cc_start: 0.8406 (tmm) cc_final: 0.8040 (tmm) REVERT: J 15 LYS cc_start: 0.8543 (mttt) cc_final: 0.7807 (ttmm) REVERT: J 21 ARG cc_start: 0.8373 (mmm160) cc_final: 0.8153 (mmm160) REVERT: J 34 ARG cc_start: 0.8585 (ttt180) cc_final: 0.7903 (tpp80) REVERT: J 61 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7670 (mt-10) REVERT: J 62 GLU cc_start: 0.8447 (mp0) cc_final: 0.8177 (mp0) REVERT: J 63 GLU cc_start: 0.8585 (pt0) cc_final: 0.8351 (pt0) REVERT: J 66 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7556 (tm-30) REVERT: J 84 ILE cc_start: 0.9308 (mt) cc_final: 0.8794 (pp) REVERT: J 89 GLU cc_start: 0.7744 (mp0) cc_final: 0.7367 (mp0) REVERT: J 100 SER cc_start: 0.8943 (t) cc_final: 0.8586 (p) REVERT: K 13 MET cc_start: 0.8115 (tmm) cc_final: 0.7855 (tmm) REVERT: K 15 LYS cc_start: 0.8403 (mttt) cc_final: 0.7810 (mtpm) REVERT: K 21 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.8300 (mtp85) REVERT: K 26 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8912 (mp) REVERT: K 62 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7825 (mp0) REVERT: K 63 GLU cc_start: 0.8802 (pt0) cc_final: 0.8593 (pt0) REVERT: K 66 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8348 (tm-30) REVERT: K 73 ILE cc_start: 0.8322 (mt) cc_final: 0.7951 (mp) REVERT: K 80 LYS cc_start: 0.8878 (tttt) cc_final: 0.8477 (tttp) REVERT: K 99 ASP cc_start: 0.8495 (t0) cc_final: 0.8213 (t70) REVERT: K 118 THR cc_start: 0.9138 (m) cc_final: 0.8700 (p) outliers start: 53 outliers final: 28 residues processed: 358 average time/residue: 1.4183 time to fit residues: 531.6026 Evaluate side-chains 359 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 322 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 30 MET Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G 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 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 30 MET Chi-restraints excluded: chain J residue 58 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.071890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051202 restraints weight = 17274.660| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.68 r_work: 0.3274 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8096 Z= 0.354 Angle : 0.809 10.013 11000 Z= 0.408 Chirality : 0.052 0.165 1287 Planarity : 0.005 0.050 1353 Dihedral : 5.796 25.319 1089 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.24 % Allowed : 25.52 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.004 0.001 HIS E 88 PHE 0.027 0.002 PHE K 64 TYR 0.021 0.002 TYR K 114 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 380 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 335 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8773 (ttt180) cc_final: 0.8188 (tpp80) REVERT: A 63 GLU cc_start: 0.8878 (pt0) cc_final: 0.7945 (pp20) REVERT: A 66 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 70 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8841 (tppp) REVERT: A 84 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9192 (pp) REVERT: A 89 GLU cc_start: 0.8345 (pm20) cc_final: 0.8013 (pm20) REVERT: A 90 HIS cc_start: 0.8393 (m90) cc_final: 0.7896 (m90) REVERT: A 104 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 106 THR cc_start: 0.9209 (m) cc_final: 0.8813 (t) REVERT: B 13 MET cc_start: 0.8204 (tmm) cc_final: 0.7694 (tmm) REVERT: B 15 LYS cc_start: 0.8691 (mttt) cc_final: 0.7943 (mtpm) REVERT: B 21 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8054 (tpp80) REVERT: B 30 MET cc_start: 0.8118 (tmm) cc_final: 0.7667 (tmm) REVERT: B 34 ARG cc_start: 0.8743 (ttt180) cc_final: 0.8150 (tpp80) REVERT: B 35 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8918 (mtpp) REVERT: B 61 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 62 GLU cc_start: 0.7851 (mp0) cc_final: 0.7109 (mp0) REVERT: B 63 GLU cc_start: 0.7867 (pm20) cc_final: 0.7429 (pm20) REVERT: B 66 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 69 TYR cc_start: 0.9419 (m-80) cc_final: 0.9156 (m-80) REVERT: B 80 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8659 (ttpt) REVERT: B 90 HIS cc_start: 0.8329 (m90) cc_final: 0.8030 (m90) REVERT: C 15 LYS cc_start: 0.8671 (mttt) cc_final: 0.8159 (mtpm) REVERT: C 18 ASP cc_start: 0.8949 (m-30) cc_final: 0.8498 (m-30) REVERT: C 30 MET cc_start: 0.8516 (ttm) cc_final: 0.8058 (tmm) REVERT: C 62 GLU cc_start: 0.7931 (mp0) cc_final: 0.7532 (mp0) REVERT: C 63 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: C 66 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (pp20) REVERT: C 90 HIS cc_start: 0.8573 (m90) cc_final: 0.8238 (m90) REVERT: D 13 MET cc_start: 0.8117 (tmm) cc_final: 0.7674 (tmm) REVERT: D 15 LYS cc_start: 0.8694 (mttt) cc_final: 0.8117 (mtpm) REVERT: D 34 ARG cc_start: 0.9034 (ttt180) cc_final: 0.8409 (tpp80) REVERT: D 61 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: D 62 GLU cc_start: 0.7867 (mp0) cc_final: 0.7579 (mp0) REVERT: D 63 GLU cc_start: 0.7842 (pm20) cc_final: 0.7499 (pm20) REVERT: D 66 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 80 LYS cc_start: 0.8987 (tttt) cc_final: 0.8639 (tttm) REVERT: D 104 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8259 (mtm-85) REVERT: D 116 TYR cc_start: 0.9463 (m-80) cc_final: 0.9171 (m-80) REVERT: E 13 MET cc_start: 0.8405 (tmm) cc_final: 0.8076 (tmm) REVERT: E 30 MET cc_start: 0.8192 (tmm) cc_final: 0.7550 (tmm) REVERT: E 34 ARG cc_start: 0.8987 (ttt180) cc_final: 0.8368 (tpp80) REVERT: E 62 GLU cc_start: 0.8475 (pm20) cc_final: 0.7302 (mp0) REVERT: E 66 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 116 TYR cc_start: 0.9391 (m-80) cc_final: 0.9083 (m-80) REVERT: F 13 MET cc_start: 0.8182 (tmm) cc_final: 0.7720 (tmm) REVERT: F 15 LYS cc_start: 0.8738 (mttt) cc_final: 0.8041 (mtpm) REVERT: F 18 ASP cc_start: 0.8884 (m-30) cc_final: 0.8493 (m-30) REVERT: F 30 MET cc_start: 0.8398 (ttm) cc_final: 0.7835 (tmm) REVERT: F 34 ARG cc_start: 0.8996 (ttt180) cc_final: 0.8287 (tpp80) REVERT: F 35 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8877 (ttmm) REVERT: F 62 GLU cc_start: 0.8318 (pm20) cc_final: 0.7557 (pm20) REVERT: F 63 GLU cc_start: 0.7929 (pm20) cc_final: 0.7068 (pm20) REVERT: F 66 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7695 (tm-30) REVERT: F 80 LYS cc_start: 0.8950 (tttt) cc_final: 0.8635 (tttp) REVERT: F 89 GLU cc_start: 0.7793 (mp0) cc_final: 0.7438 (mp0) REVERT: G 13 MET cc_start: 0.8636 (tmm) cc_final: 0.7995 (tmm) REVERT: G 15 LYS cc_start: 0.8994 (mttt) cc_final: 0.8329 (mttp) REVERT: G 30 MET cc_start: 0.8243 (tmm) cc_final: 0.7473 (tmm) REVERT: G 34 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8311 (tpp80) REVERT: G 63 GLU cc_start: 0.8531 (pt0) cc_final: 0.7499 (pm20) REVERT: G 66 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7538 (tm-30) REVERT: G 104 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8046 (ttm110) REVERT: H 15 LYS cc_start: 0.8675 (mttt) cc_final: 0.8020 (mtpp) REVERT: H 30 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7878 (tmm) REVERT: H 34 ARG cc_start: 0.8954 (ttt180) cc_final: 0.8329 (tpp80) REVERT: H 62 GLU cc_start: 0.8281 (mp0) cc_final: 0.7791 (mp0) REVERT: H 63 GLU cc_start: 0.8755 (pt0) cc_final: 0.8007 (pm20) REVERT: H 66 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7533 (tm-30) REVERT: H 70 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9048 (ttpp) REVERT: H 84 ILE cc_start: 0.9354 (mt) cc_final: 0.8853 (pp) REVERT: H 89 GLU cc_start: 0.8060 (mp0) cc_final: 0.7751 (pm20) REVERT: I 13 MET cc_start: 0.8132 (tmm) cc_final: 0.7651 (tmm) REVERT: I 15 LYS cc_start: 0.8744 (mttt) cc_final: 0.7966 (mtpp) REVERT: I 30 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8154 (tmm) REVERT: I 34 ARG cc_start: 0.8798 (ttt180) cc_final: 0.8406 (tpp80) REVERT: I 70 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9141 (tppp) REVERT: I 72 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8355 (mp0) REVERT: I 80 LYS cc_start: 0.8882 (tttt) cc_final: 0.8522 (tttp) REVERT: I 99 ASP cc_start: 0.8859 (t0) cc_final: 0.8323 (t70) REVERT: I 100 SER cc_start: 0.8803 (t) cc_final: 0.8530 (p) REVERT: I 104 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7864 (ttm110) REVERT: J 13 MET cc_start: 0.8457 (tmm) cc_final: 0.8129 (tmm) REVERT: J 15 LYS cc_start: 0.8603 (mttt) cc_final: 0.7848 (ttmm) REVERT: J 21 ARG cc_start: 0.8391 (mmm160) cc_final: 0.8174 (mmm160) REVERT: J 30 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: J 34 ARG cc_start: 0.8609 (ttt180) cc_final: 0.7990 (tpp80) REVERT: J 35 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8626 (mtpp) REVERT: J 63 GLU cc_start: 0.8618 (pt0) cc_final: 0.8395 (pt0) REVERT: J 66 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7617 (tm-30) REVERT: J 84 ILE cc_start: 0.9332 (mt) cc_final: 0.8813 (pp) REVERT: J 89 GLU cc_start: 0.7806 (mp0) cc_final: 0.6508 (mp0) REVERT: J 100 SER cc_start: 0.8936 (t) cc_final: 0.8549 (p) REVERT: K 13 MET cc_start: 0.8190 (tmm) cc_final: 0.7909 (tmm) REVERT: K 15 LYS cc_start: 0.8465 (mttt) cc_final: 0.7847 (mtpm) REVERT: K 21 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8325 (mtp85) REVERT: K 26 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8934 (mp) REVERT: K 62 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7769 (mp0) REVERT: K 63 GLU cc_start: 0.8788 (pt0) cc_final: 0.8585 (pt0) REVERT: K 66 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8285 (tm-30) REVERT: K 80 LYS cc_start: 0.8881 (tttt) cc_final: 0.8506 (tttm) REVERT: K 99 ASP cc_start: 0.8511 (t0) cc_final: 0.8232 (t70) REVERT: K 118 THR cc_start: 0.9169 (m) cc_final: 0.8670 (p) outliers start: 45 outliers final: 23 residues processed: 357 average time/residue: 1.4442 time to fit residues: 540.4367 Evaluate side-chains 359 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 326 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 61 GLU 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 G residue 70 LYS Chi-restraints excluded: chain G 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 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 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 30 MET Chi-restraints excluded: chain J residue 58 LEU 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 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: 5.9990 chunk 21 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN K 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.070015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.050972 restraints weight = 17472.717| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.70 r_work: 0.3284 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8096 Z= 0.341 Angle : 0.817 10.020 11000 Z= 0.410 Chirality : 0.052 0.254 1287 Planarity : 0.006 0.054 1353 Dihedral : 5.764 25.539 1089 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.66 % Allowed : 28.32 % Favored : 67.02 % 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: -2.81 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.002 0.001 HIS C 88 PHE 0.027 0.002 PHE K 64 TYR 0.019 0.002 TYR K 114 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 : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8794 (ttt180) cc_final: 0.8199 (tpp80) REVERT: A 63 GLU cc_start: 0.8870 (pt0) cc_final: 0.8155 (pp20) REVERT: A 66 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 70 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8852 (tppp) REVERT: A 90 HIS cc_start: 0.8455 (m90) cc_final: 0.8157 (m90) REVERT: A 104 ARG cc_start: 0.8089 (mtm-85) cc_final: 0.7311 (mtm-85) REVERT: A 106 THR cc_start: 0.9193 (m) cc_final: 0.8806 (t) REVERT: B 13 MET cc_start: 0.8237 (tmm) cc_final: 0.7437 (tmm) REVERT: B 15 LYS cc_start: 0.8676 (mttt) cc_final: 0.7960 (mtpm) REVERT: B 18 ASP cc_start: 0.9017 (m-30) cc_final: 0.8279 (m-30) REVERT: B 21 ARG cc_start: 0.8480 (mtp85) cc_final: 0.8037 (tpp80) REVERT: B 30 MET cc_start: 0.8176 (tmm) cc_final: 0.7592 (tmm) REVERT: B 34 ARG cc_start: 0.8729 (ttt180) cc_final: 0.8149 (tpp80) REVERT: B 35 LYS cc_start: 0.9101 (ttmt) cc_final: 0.8861 (mtpp) REVERT: B 61 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 62 GLU cc_start: 0.7767 (mp0) cc_final: 0.7233 (mp0) REVERT: B 66 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7627 (tm-30) REVERT: B 69 TYR cc_start: 0.9409 (m-80) cc_final: 0.9165 (m-80) REVERT: B 80 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8644 (ttpt) REVERT: C 15 LYS cc_start: 0.8633 (mttt) cc_final: 0.8108 (mtpm) REVERT: C 18 ASP cc_start: 0.8961 (m-30) cc_final: 0.8554 (m-30) REVERT: C 30 MET cc_start: 0.8475 (ttm) cc_final: 0.8075 (tmm) REVERT: C 35 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8830 (mtmt) REVERT: C 62 GLU cc_start: 0.7929 (mp0) cc_final: 0.7397 (mp0) REVERT: C 63 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: C 66 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (pp20) REVERT: C 90 HIS cc_start: 0.8541 (m90) cc_final: 0.8237 (m90) REVERT: D 13 MET cc_start: 0.8086 (tmm) cc_final: 0.7620 (tmm) REVERT: D 15 LYS cc_start: 0.8669 (mttt) cc_final: 0.8009 (mtpm) REVERT: D 34 ARG cc_start: 0.9025 (ttt180) cc_final: 0.8374 (tpp80) REVERT: D 61 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: D 63 GLU cc_start: 0.7853 (pm20) cc_final: 0.7295 (pm20) REVERT: D 66 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7799 (tm-30) REVERT: D 80 LYS cc_start: 0.8965 (tttt) cc_final: 0.8612 (tttp) REVERT: D 104 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8239 (mtm-85) REVERT: D 116 TYR cc_start: 0.9469 (m-80) cc_final: 0.9218 (m-80) REVERT: E 13 MET cc_start: 0.8408 (tmm) cc_final: 0.8054 (tmm) REVERT: E 30 MET cc_start: 0.8180 (tmm) cc_final: 0.7541 (tmm) REVERT: E 34 ARG cc_start: 0.8984 (ttt180) cc_final: 0.8385 (tpp80) REVERT: E 62 GLU cc_start: 0.8503 (pm20) cc_final: 0.7309 (mp0) REVERT: E 63 GLU cc_start: 0.8028 (pm20) cc_final: 0.7768 (pm20) REVERT: E 66 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7643 (tm-30) REVERT: F 13 MET cc_start: 0.8217 (tmm) cc_final: 0.7699 (tmm) REVERT: F 15 LYS cc_start: 0.8737 (mttt) cc_final: 0.8017 (mtpm) REVERT: F 18 ASP cc_start: 0.8903 (m-30) cc_final: 0.8538 (m-30) REVERT: F 30 MET cc_start: 0.8373 (ttm) cc_final: 0.7845 (tmm) REVERT: F 34 ARG cc_start: 0.8985 (ttt180) cc_final: 0.8278 (tpp80) REVERT: F 35 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8877 (ttmm) REVERT: F 62 GLU cc_start: 0.8279 (pm20) cc_final: 0.7476 (pm20) REVERT: F 63 GLU cc_start: 0.7888 (pm20) cc_final: 0.7134 (pm20) REVERT: F 66 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7791 (tm-30) REVERT: F 80 LYS cc_start: 0.8934 (tttt) cc_final: 0.8621 (tttm) REVERT: F 89 GLU cc_start: 0.7790 (mp0) cc_final: 0.7359 (mp0) REVERT: G 13 MET cc_start: 0.8625 (tmm) cc_final: 0.7939 (tmm) REVERT: G 15 LYS cc_start: 0.8960 (mttt) cc_final: 0.8256 (mttp) REVERT: G 30 MET cc_start: 0.8311 (tmm) cc_final: 0.7461 (tmm) REVERT: G 34 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8310 (tpp80) REVERT: G 63 GLU cc_start: 0.8519 (pt0) cc_final: 0.7530 (pm20) REVERT: G 66 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7494 (tm-30) REVERT: G 104 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8025 (ttm110) REVERT: H 15 LYS cc_start: 0.8657 (mttt) cc_final: 0.8069 (mtpp) REVERT: H 30 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7890 (tmm) REVERT: H 34 ARG cc_start: 0.8943 (ttt180) cc_final: 0.8313 (tpp80) REVERT: H 62 GLU cc_start: 0.8257 (mp0) cc_final: 0.7788 (mp0) REVERT: H 63 GLU cc_start: 0.8724 (pt0) cc_final: 0.8001 (pm20) REVERT: H 66 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7660 (tm-30) REVERT: H 84 ILE cc_start: 0.9334 (mt) cc_final: 0.8843 (pp) REVERT: I 13 MET cc_start: 0.8077 (tmm) cc_final: 0.7682 (tmm) REVERT: I 15 LYS cc_start: 0.8646 (mttt) cc_final: 0.7894 (mtpm) REVERT: I 30 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8118 (tmm) REVERT: I 34 ARG cc_start: 0.8784 (ttt180) cc_final: 0.8404 (tpp80) REVERT: I 70 LYS cc_start: 0.9340 (ttmm) cc_final: 0.9075 (tppp) REVERT: I 72 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8309 (mp0) REVERT: I 80 LYS cc_start: 0.8869 (tttt) cc_final: 0.8502 (tttm) REVERT: I 99 ASP cc_start: 0.8873 (t0) cc_final: 0.8316 (t70) REVERT: I 100 SER cc_start: 0.8798 (t) cc_final: 0.8534 (p) REVERT: I 104 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7843 (ttm110) REVERT: J 13 MET cc_start: 0.8451 (tmm) cc_final: 0.8086 (tmm) REVERT: J 15 LYS cc_start: 0.8580 (mttt) cc_final: 0.7811 (ttmm) REVERT: J 21 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8168 (mmm160) REVERT: J 30 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: J 34 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8209 (ttt-90) REVERT: J 35 LYS cc_start: 0.9055 (ttmt) cc_final: 0.8654 (mtpp) REVERT: J 61 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: J 62 GLU cc_start: 0.8358 (mp0) cc_final: 0.8110 (mp0) REVERT: J 63 GLU cc_start: 0.8630 (pt0) cc_final: 0.8426 (pt0) REVERT: J 66 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7444 (tm-30) REVERT: J 84 ILE cc_start: 0.9318 (mt) cc_final: 0.8790 (pp) REVERT: J 100 SER cc_start: 0.8928 (t) cc_final: 0.8547 (p) REVERT: K 13 MET cc_start: 0.8153 (tmm) cc_final: 0.7865 (tmm) REVERT: K 15 LYS cc_start: 0.8434 (mttt) cc_final: 0.7813 (mtpm) REVERT: K 21 ARG cc_start: 0.8537 (mmm-85) cc_final: 0.8317 (mtp85) REVERT: K 26 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8914 (mp) REVERT: K 62 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7778 (mp0) REVERT: K 66 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8129 (tm-30) REVERT: K 76 LYS cc_start: 0.8166 (mtmm) cc_final: 0.7833 (mptt) REVERT: K 80 LYS cc_start: 0.8879 (tttt) cc_final: 0.8501 (tttm) REVERT: K 99 ASP cc_start: 0.8523 (t0) cc_final: 0.8020 (t70) REVERT: K 118 THR cc_start: 0.9156 (m) cc_final: 0.8648 (p) outliers start: 40 outliers final: 24 residues processed: 351 average time/residue: 1.4538 time to fit residues: 534.5816 Evaluate side-chains 358 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU 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 68 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G 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 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 30 MET Chi-restraints excluded: chain J residue 61 GLU 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 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: 9.9990 chunk 95 optimal weight: 0.0020 chunk 62 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 14 optimal weight: 0.0470 chunk 52 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN K 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.071201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.052199 restraints weight = 17226.137| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.65 r_work: 0.3294 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8096 Z= 0.328 Angle : 0.858 10.667 11000 Z= 0.429 Chirality : 0.053 0.237 1287 Planarity : 0.006 0.070 1353 Dihedral : 5.735 25.268 1089 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.90 % Allowed : 29.37 % Favored : 65.73 % 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 (0.23), 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 0.003 0.001 TRP E 79 HIS 0.003 0.001 HIS E 88 PHE 0.026 0.002 PHE K 64 TYR 0.019 0.002 TYR I 116 ARG 0.019 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 384 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 342 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8827 (ttt180) cc_final: 0.8243 (tpp80) REVERT: A 63 GLU cc_start: 0.8888 (pt0) cc_final: 0.7911 (pp20) REVERT: A 66 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 70 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8842 (tppp) REVERT: A 90 HIS cc_start: 0.8543 (m90) cc_final: 0.8066 (m90) REVERT: A 104 ARG cc_start: 0.8147 (mtm-85) cc_final: 0.7811 (mtt90) REVERT: A 106 THR cc_start: 0.9201 (m) cc_final: 0.8823 (t) REVERT: B 13 MET cc_start: 0.8001 (tmm) cc_final: 0.7554 (tmm) REVERT: B 15 LYS cc_start: 0.8659 (mttt) cc_final: 0.7890 (mtpm) REVERT: B 18 ASP cc_start: 0.9037 (m-30) cc_final: 0.8235 (m-30) REVERT: B 21 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8004 (tpp80) REVERT: B 30 MET cc_start: 0.8280 (tmm) cc_final: 0.7779 (tmm) REVERT: B 34 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8145 (tpp80) REVERT: B 35 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8846 (mtpp) REVERT: B 61 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 62 GLU cc_start: 0.7944 (mp0) cc_final: 0.7099 (mp0) REVERT: B 63 GLU cc_start: 0.7837 (pm20) cc_final: 0.7463 (pm20) REVERT: B 66 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 69 TYR cc_start: 0.9397 (m-80) cc_final: 0.9168 (m-80) REVERT: B 80 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8610 (ttpt) REVERT: C 15 LYS cc_start: 0.8678 (mttt) cc_final: 0.8177 (mtpm) REVERT: C 18 ASP cc_start: 0.8966 (m-30) cc_final: 0.8533 (m-30) REVERT: C 21 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8330 (mtp85) REVERT: C 30 MET cc_start: 0.8505 (ttm) cc_final: 0.8173 (tmm) REVERT: C 35 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8916 (mtmt) REVERT: C 62 GLU cc_start: 0.7988 (mp0) cc_final: 0.7645 (mp0) REVERT: C 63 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: C 66 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: C 90 HIS cc_start: 0.8566 (m90) cc_final: 0.8183 (m90) REVERT: D 13 MET cc_start: 0.8137 (tmm) cc_final: 0.7682 (tmm) REVERT: D 15 LYS cc_start: 0.8711 (mttt) cc_final: 0.8069 (mtpm) REVERT: D 34 ARG cc_start: 0.9028 (ttt180) cc_final: 0.8402 (tpp80) REVERT: D 63 GLU cc_start: 0.7913 (pm20) cc_final: 0.7620 (pm20) REVERT: D 66 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 80 LYS cc_start: 0.8983 (tttt) cc_final: 0.8618 (tttm) REVERT: D 104 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.8240 (mtm-85) REVERT: D 116 TYR cc_start: 0.9465 (m-80) cc_final: 0.9258 (m-80) REVERT: E 13 MET cc_start: 0.8433 (tmm) cc_final: 0.8067 (tmm) REVERT: E 30 MET cc_start: 0.8318 (tmm) cc_final: 0.7582 (tmm) REVERT: E 34 ARG cc_start: 0.9010 (ttt180) cc_final: 0.8460 (tpp80) REVERT: E 62 GLU cc_start: 0.8335 (pm20) cc_final: 0.7634 (mp0) REVERT: E 66 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7628 (tm-30) REVERT: E 116 TYR cc_start: 0.9399 (m-80) cc_final: 0.9141 (m-80) REVERT: F 13 MET cc_start: 0.8237 (tmm) cc_final: 0.7674 (tmm) REVERT: F 15 LYS cc_start: 0.8758 (mttt) cc_final: 0.8039 (mtpm) REVERT: F 18 ASP cc_start: 0.8941 (m-30) cc_final: 0.8571 (m-30) REVERT: F 30 MET cc_start: 0.8433 (ttm) cc_final: 0.7920 (tmm) REVERT: F 34 ARG cc_start: 0.9018 (ttt180) cc_final: 0.8308 (tpp80) REVERT: F 35 LYS cc_start: 0.9271 (ttpt) cc_final: 0.8918 (ttmm) REVERT: F 62 GLU cc_start: 0.8377 (pm20) cc_final: 0.7582 (pm20) REVERT: F 63 GLU cc_start: 0.7950 (pm20) cc_final: 0.7132 (pm20) REVERT: F 66 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7867 (tm-30) REVERT: F 80 LYS cc_start: 0.8973 (tttt) cc_final: 0.8668 (tttm) REVERT: G 13 MET cc_start: 0.8623 (tmm) cc_final: 0.7944 (tmm) REVERT: G 15 LYS cc_start: 0.8973 (mttt) cc_final: 0.8338 (mttp) REVERT: G 30 MET cc_start: 0.8468 (tmm) cc_final: 0.7733 (tmm) REVERT: G 34 ARG cc_start: 0.8940 (ttt180) cc_final: 0.8312 (tpp80) REVERT: G 61 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: G 63 GLU cc_start: 0.8529 (pt0) cc_final: 0.7497 (pm20) REVERT: G 66 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7684 (tm-30) REVERT: G 104 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.8024 (ttm110) REVERT: H 15 LYS cc_start: 0.8688 (mttt) cc_final: 0.8147 (mtpp) REVERT: H 30 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7898 (tmm) REVERT: H 34 ARG cc_start: 0.8988 (ttt180) cc_final: 0.8457 (tpp80) REVERT: H 35 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8638 (mttt) REVERT: H 62 GLU cc_start: 0.8322 (mp0) cc_final: 0.7818 (mp0) REVERT: H 63 GLU cc_start: 0.8735 (pt0) cc_final: 0.8095 (pm20) REVERT: H 66 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7803 (tm-30) REVERT: H 84 ILE cc_start: 0.9369 (mt) cc_final: 0.8874 (pp) REVERT: H 89 GLU cc_start: 0.7956 (mp0) cc_final: 0.7677 (mp0) REVERT: I 13 MET cc_start: 0.8205 (tmm) cc_final: 0.7888 (tmm) REVERT: I 18 ASP cc_start: 0.8818 (m-30) cc_final: 0.8466 (m-30) REVERT: I 30 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8197 (tmm) REVERT: I 34 ARG cc_start: 0.8822 (ttt180) cc_final: 0.8436 (tpp80) REVERT: I 80 LYS cc_start: 0.8897 (tttt) cc_final: 0.8512 (tttm) REVERT: I 99 ASP cc_start: 0.8861 (t0) cc_final: 0.8334 (t70) REVERT: I 100 SER cc_start: 0.8797 (t) cc_final: 0.8535 (p) REVERT: I 104 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7858 (ttm110) REVERT: J 13 MET cc_start: 0.8482 (tmm) cc_final: 0.8111 (tmm) REVERT: J 15 LYS cc_start: 0.8643 (mttt) cc_final: 0.7912 (ttmm) REVERT: J 21 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8186 (mmm160) REVERT: J 30 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8175 (mmm) REVERT: J 34 ARG cc_start: 0.8650 (ttt180) cc_final: 0.8324 (ttt-90) REVERT: J 35 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8761 (ttmm) REVERT: J 66 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7494 (tm-30) REVERT: J 84 ILE cc_start: 0.9358 (mt) cc_final: 0.8832 (pp) REVERT: J 100 SER cc_start: 0.8946 (t) cc_final: 0.8568 (p) REVERT: K 13 MET cc_start: 0.8252 (tmm) cc_final: 0.7949 (tmm) REVERT: K 15 LYS cc_start: 0.8548 (mttt) cc_final: 0.7931 (mtpm) REVERT: K 21 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8340 (mtp85) REVERT: K 26 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8929 (mp) REVERT: K 62 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7826 (mp0) REVERT: K 66 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8108 (tm-30) REVERT: K 73 ILE cc_start: 0.8323 (mt) cc_final: 0.8012 (mp) REVERT: K 76 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7951 (mptt) REVERT: K 80 LYS cc_start: 0.8895 (tttt) cc_final: 0.8515 (tttm) REVERT: K 99 ASP cc_start: 0.8430 (t0) cc_final: 0.7955 (t70) REVERT: K 118 THR cc_start: 0.9163 (m) cc_final: 0.8659 (p) outliers start: 42 outliers final: 21 residues processed: 360 average time/residue: 1.4435 time to fit residues: 543.9411 Evaluate side-chains 358 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 82 LEU 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 58 LEU 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 61 GLU 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 J residue 30 MET Chi-restraints excluded: chain J residue 106 THR 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: 6.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.072528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.053321 restraints weight = 17330.001| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.74 r_work: 0.3324 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8096 Z= 0.288 Angle : 0.895 11.840 11000 Z= 0.447 Chirality : 0.052 0.188 1287 Planarity : 0.006 0.073 1353 Dihedral : 5.702 24.504 1089 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 32.05 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.93 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS B 31 PHE 0.025 0.001 PHE K 64 TYR 0.017 0.002 TYR J 105 ARG 0.020 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 374 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 342 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8955 (tpp) cc_final: 0.8230 (tpt) REVERT: A 34 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8139 (tpp80) REVERT: A 63 GLU cc_start: 0.8906 (pt0) cc_final: 0.8126 (pp20) REVERT: A 66 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7807 (tm-30) REVERT: A 70 LYS cc_start: 0.9105 (tppp) cc_final: 0.8877 (tppp) REVERT: A 90 HIS cc_start: 0.8616 (m90) cc_final: 0.8207 (m90) REVERT: A 104 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7820 (mtt90) REVERT: A 106 THR cc_start: 0.9232 (m) cc_final: 0.8910 (p) REVERT: B 13 MET cc_start: 0.7927 (tmm) cc_final: 0.7408 (tmm) REVERT: B 15 LYS cc_start: 0.8697 (mttt) cc_final: 0.8083 (mtpm) REVERT: B 18 ASP cc_start: 0.9035 (m-30) cc_final: 0.8567 (m-30) REVERT: B 21 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8006 (tpp80) REVERT: B 30 MET cc_start: 0.8325 (tmm) cc_final: 0.7889 (tmm) REVERT: B 34 ARG cc_start: 0.8750 (ttt180) cc_final: 0.8038 (tpp80) REVERT: B 35 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8834 (mtpp) REVERT: B 61 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 62 GLU cc_start: 0.7974 (mp0) cc_final: 0.7287 (mp0) REVERT: B 66 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 69 TYR cc_start: 0.9362 (m-80) cc_final: 0.9102 (m-80) REVERT: B 80 LYS cc_start: 0.9019 (ttpt) cc_final: 0.8615 (ttpt) REVERT: C 15 LYS cc_start: 0.8691 (mttt) cc_final: 0.8208 (mtpm) REVERT: C 18 ASP cc_start: 0.8918 (m-30) cc_final: 0.8440 (m-30) REVERT: C 21 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8353 (mtp85) REVERT: C 30 MET cc_start: 0.8486 (ttm) cc_final: 0.8133 (tmm) REVERT: C 35 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8875 (mttt) REVERT: C 62 GLU cc_start: 0.8008 (mp0) cc_final: 0.7571 (mp0) REVERT: C 63 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: C 70 LYS cc_start: 0.9167 (ptmm) cc_final: 0.8936 (ptmm) REVERT: C 90 HIS cc_start: 0.8537 (m90) cc_final: 0.8200 (m90) REVERT: C 104 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: D 13 MET cc_start: 0.8079 (tmm) cc_final: 0.7620 (tmm) REVERT: D 15 LYS cc_start: 0.8714 (mttt) cc_final: 0.8083 (mtpm) REVERT: D 34 ARG cc_start: 0.9033 (ttt180) cc_final: 0.8355 (tpp80) REVERT: D 58 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (tp) REVERT: D 61 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: D 63 GLU cc_start: 0.7857 (pm20) cc_final: 0.7254 (pm20) REVERT: D 66 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 80 LYS cc_start: 0.8993 (tttt) cc_final: 0.8627 (tttp) REVERT: D 104 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8083 (mtm-85) REVERT: D 116 TYR cc_start: 0.9469 (m-80) cc_final: 0.9265 (m-80) REVERT: E 13 MET cc_start: 0.8438 (tmm) cc_final: 0.8062 (tmm) REVERT: E 30 MET cc_start: 0.8345 (tmm) cc_final: 0.7591 (tmm) REVERT: E 34 ARG cc_start: 0.9062 (ttt180) cc_final: 0.8459 (tpp80) REVERT: E 62 GLU cc_start: 0.8499 (pm20) cc_final: 0.7503 (mp0) REVERT: E 63 GLU cc_start: 0.8034 (pm20) cc_final: 0.7740 (pm20) REVERT: E 66 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7620 (tm-30) REVERT: E 89 GLU cc_start: 0.8421 (mp0) cc_final: 0.8182 (mp0) REVERT: E 116 TYR cc_start: 0.9399 (m-80) cc_final: 0.9163 (m-80) REVERT: F 13 MET cc_start: 0.8258 (tmm) cc_final: 0.7702 (tmm) REVERT: F 15 LYS cc_start: 0.8765 (mttt) cc_final: 0.8057 (mtpm) REVERT: F 18 ASP cc_start: 0.8912 (m-30) cc_final: 0.8539 (m-30) REVERT: F 30 MET cc_start: 0.8401 (ttm) cc_final: 0.7893 (tmm) REVERT: F 34 ARG cc_start: 0.9007 (ttt180) cc_final: 0.8290 (tpp80) REVERT: F 35 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8915 (ttmm) REVERT: F 62 GLU cc_start: 0.8356 (pm20) cc_final: 0.7537 (pm20) REVERT: F 63 GLU cc_start: 0.7931 (pm20) cc_final: 0.7063 (pm20) REVERT: F 66 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7883 (tm-30) REVERT: F 80 LYS cc_start: 0.8987 (tttt) cc_final: 0.8685 (tttp) REVERT: F 89 GLU cc_start: 0.8109 (mp0) cc_final: 0.7822 (mp0) REVERT: G 13 MET cc_start: 0.8612 (tmm) cc_final: 0.7929 (tmm) REVERT: G 15 LYS cc_start: 0.8973 (mttt) cc_final: 0.8347 (mttp) REVERT: G 30 MET cc_start: 0.8499 (tmm) cc_final: 0.7766 (tmm) REVERT: G 34 ARG cc_start: 0.8937 (ttt180) cc_final: 0.8311 (tpp80) REVERT: G 62 GLU cc_start: 0.8152 (mp0) cc_final: 0.7907 (mp0) REVERT: G 63 GLU cc_start: 0.8508 (pt0) cc_final: 0.7397 (pm20) REVERT: G 66 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7726 (tm-30) REVERT: G 72 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8306 (mp0) REVERT: G 104 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8024 (ttm110) REVERT: H 15 LYS cc_start: 0.8690 (mttt) cc_final: 0.8172 (mtpp) REVERT: H 30 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: H 34 ARG cc_start: 0.9007 (ttt180) cc_final: 0.8406 (tpp80) REVERT: H 62 GLU cc_start: 0.8403 (mp0) cc_final: 0.7721 (mp0) REVERT: H 63 GLU cc_start: 0.8706 (pt0) cc_final: 0.8091 (pm20) REVERT: H 66 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7568 (tm-30) REVERT: H 70 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8819 (ttpp) REVERT: H 72 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8259 (mp0) REVERT: H 84 ILE cc_start: 0.9389 (mt) cc_final: 0.8911 (pp) REVERT: H 89 GLU cc_start: 0.7982 (mp0) cc_final: 0.7716 (mp0) REVERT: I 13 MET cc_start: 0.8138 (tmm) cc_final: 0.7825 (tmm) REVERT: I 18 ASP cc_start: 0.8865 (m-30) cc_final: 0.8496 (m-30) REVERT: I 30 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8216 (tmm) REVERT: I 34 ARG cc_start: 0.8825 (ttt180) cc_final: 0.8461 (tpp80) REVERT: I 72 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8343 (mp0) REVERT: I 80 LYS cc_start: 0.8897 (tttt) cc_final: 0.8531 (tttm) REVERT: I 99 ASP cc_start: 0.8840 (t0) cc_final: 0.8343 (t70) REVERT: I 100 SER cc_start: 0.8797 (t) cc_final: 0.8503 (p) REVERT: I 104 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7820 (ttm110) REVERT: J 13 MET cc_start: 0.8512 (tmm) cc_final: 0.8162 (tmm) REVERT: J 15 LYS cc_start: 0.8652 (mttt) cc_final: 0.7900 (ttmm) REVERT: J 21 ARG cc_start: 0.8408 (mmm160) cc_final: 0.8193 (mmm160) REVERT: J 30 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: J 34 ARG cc_start: 0.8675 (ttt180) cc_final: 0.8306 (ttt-90) REVERT: J 35 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8364 (mttm) REVERT: J 66 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7546 (tm-30) REVERT: J 84 ILE cc_start: 0.9360 (mt) cc_final: 0.8877 (pp) REVERT: J 100 SER cc_start: 0.8907 (t) cc_final: 0.8531 (p) REVERT: K 13 MET cc_start: 0.8236 (tmm) cc_final: 0.7932 (tmm) REVERT: K 15 LYS cc_start: 0.8567 (mttt) cc_final: 0.7934 (mtpm) REVERT: K 21 ARG cc_start: 0.8554 (mmm-85) cc_final: 0.8330 (mtp85) REVERT: K 26 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8922 (mp) REVERT: K 62 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7849 (mp0) REVERT: K 66 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8104 (tm-30) REVERT: K 73 ILE cc_start: 0.8322 (mt) cc_final: 0.7998 (mp) REVERT: K 76 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8062 (mptt) REVERT: K 80 LYS cc_start: 0.8893 (tttt) cc_final: 0.8504 (tttm) REVERT: K 99 ASP cc_start: 0.8431 (t0) cc_final: 0.8087 (t70) REVERT: K 118 THR cc_start: 0.9191 (m) cc_final: 0.8686 (p) outliers start: 32 outliers final: 20 residues processed: 354 average time/residue: 1.4272 time to fit residues: 529.3480 Evaluate side-chains 356 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 26 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU 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 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 12 LEU 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 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 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 2 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN K 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.071004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.052181 restraints weight = 17263.320| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.64 r_work: 0.3297 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8096 Z= 0.373 Angle : 0.934 12.084 11000 Z= 0.468 Chirality : 0.053 0.158 1287 Planarity : 0.007 0.082 1353 Dihedral : 5.777 25.992 1089 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.38 % Allowed : 32.05 % Favored : 64.57 % 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 (0.23), 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 0.005 0.001 TRP C 79 HIS 0.002 0.001 HIS B 90 PHE 0.024 0.002 PHE K 64 TYR 0.019 0.002 TYR I 116 ARG 0.020 0.002 ARG K 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: 29 poor density : 329 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8819 (ttt180) cc_final: 0.8230 (tpp80) REVERT: A 63 GLU cc_start: 0.8927 (pt0) cc_final: 0.7968 (pp20) REVERT: A 66 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 70 LYS cc_start: 0.9090 (tppp) cc_final: 0.8863 (tppp) REVERT: A 90 HIS cc_start: 0.8669 (m90) cc_final: 0.8296 (m90) REVERT: A 104 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7777 (mtt90) REVERT: A 106 THR cc_start: 0.9228 (m) cc_final: 0.8881 (t) REVERT: B 13 MET cc_start: 0.7862 (tmm) cc_final: 0.7503 (tmm) REVERT: B 18 ASP cc_start: 0.9043 (m-30) cc_final: 0.8640 (m-30) REVERT: B 21 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8021 (tpp80) REVERT: B 30 MET cc_start: 0.8339 (tmm) cc_final: 0.7892 (tmm) REVERT: B 34 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8131 (tpp80) REVERT: B 35 LYS cc_start: 0.9067 (ttmt) cc_final: 0.8832 (mtpp) REVERT: B 62 GLU cc_start: 0.8044 (mp0) cc_final: 0.7506 (mp0) REVERT: B 63 GLU cc_start: 0.7823 (pm20) cc_final: 0.7455 (pm20) REVERT: B 66 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 69 TYR cc_start: 0.9377 (m-80) cc_final: 0.9150 (m-80) REVERT: B 80 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8604 (ttpt) REVERT: C 15 LYS cc_start: 0.8684 (mttt) cc_final: 0.8157 (mtpm) REVERT: C 18 ASP cc_start: 0.8904 (m-30) cc_final: 0.8478 (m-30) REVERT: C 21 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8362 (mtp85) REVERT: C 30 MET cc_start: 0.8513 (ttm) cc_final: 0.8124 (tmm) REVERT: C 35 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8867 (mttt) REVERT: C 63 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: C 69 TYR cc_start: 0.9317 (m-80) cc_final: 0.9096 (m-80) REVERT: C 70 LYS cc_start: 0.9161 (ptmm) cc_final: 0.8927 (ptmm) REVERT: C 90 HIS cc_start: 0.8461 (m90) cc_final: 0.8079 (m90) REVERT: D 13 MET cc_start: 0.8096 (tmm) cc_final: 0.7646 (tmm) REVERT: D 15 LYS cc_start: 0.8704 (mttt) cc_final: 0.8067 (mtpm) REVERT: D 34 ARG cc_start: 0.9037 (ttt180) cc_final: 0.8419 (tpp80) REVERT: D 58 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8613 (tp) REVERT: D 63 GLU cc_start: 0.7839 (pm20) cc_final: 0.7066 (pm20) REVERT: D 66 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7831 (tm-30) REVERT: D 80 LYS cc_start: 0.8984 (tttt) cc_final: 0.8623 (tttp) REVERT: D 104 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8254 (mtm-85) REVERT: D 116 TYR cc_start: 0.9466 (m-80) cc_final: 0.9256 (m-80) REVERT: E 13 MET cc_start: 0.8415 (tmm) cc_final: 0.8034 (tmm) REVERT: E 18 ASP cc_start: 0.8843 (m-30) cc_final: 0.8398 (m-30) REVERT: E 30 MET cc_start: 0.8363 (tmm) cc_final: 0.7574 (tmm) REVERT: E 34 ARG cc_start: 0.9044 (ttt180) cc_final: 0.8428 (tpp80) REVERT: E 62 GLU cc_start: 0.8461 (pm20) cc_final: 0.7599 (mp0) REVERT: E 63 GLU cc_start: 0.8046 (pm20) cc_final: 0.7735 (pm20) REVERT: E 66 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7589 (tm-30) REVERT: E 89 GLU cc_start: 0.8383 (mp0) cc_final: 0.8162 (mp0) REVERT: E 116 TYR cc_start: 0.9407 (m-80) cc_final: 0.9156 (m-80) REVERT: F 13 MET cc_start: 0.8241 (tmm) cc_final: 0.7640 (tmm) REVERT: F 15 LYS cc_start: 0.8767 (mttt) cc_final: 0.8029 (mtpm) REVERT: F 18 ASP cc_start: 0.8908 (m-30) cc_final: 0.8540 (m-30) REVERT: F 30 MET cc_start: 0.8442 (ttm) cc_final: 0.7875 (tmm) REVERT: F 34 ARG cc_start: 0.9006 (ttt180) cc_final: 0.8290 (tpp80) REVERT: F 35 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8885 (ttmm) REVERT: F 62 GLU cc_start: 0.8409 (pm20) cc_final: 0.7626 (pm20) REVERT: F 63 GLU cc_start: 0.7948 (pm20) cc_final: 0.7079 (pm20) REVERT: F 66 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7884 (tm-30) REVERT: F 72 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8516 (mm-30) REVERT: F 80 LYS cc_start: 0.8974 (tttt) cc_final: 0.8673 (tttp) REVERT: F 89 GLU cc_start: 0.8021 (mp0) cc_final: 0.7776 (mp0) REVERT: G 13 MET cc_start: 0.8631 (tmm) cc_final: 0.7910 (tmm) REVERT: G 15 LYS cc_start: 0.8960 (mttt) cc_final: 0.8344 (mttp) REVERT: G 30 MET cc_start: 0.8539 (tmm) cc_final: 0.7751 (tmm) REVERT: G 34 ARG cc_start: 0.8920 (ttt180) cc_final: 0.8304 (tpp80) REVERT: G 62 GLU cc_start: 0.8134 (mp0) cc_final: 0.7880 (mp0) REVERT: G 63 GLU cc_start: 0.8505 (pt0) cc_final: 0.7409 (pm20) REVERT: G 66 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7704 (tm-30) REVERT: G 72 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8284 (mp0) REVERT: G 104 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8027 (ttm110) REVERT: H 15 LYS cc_start: 0.8677 (mttt) cc_final: 0.8131 (mtpp) REVERT: H 30 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7905 (tmm) REVERT: H 34 ARG cc_start: 0.9011 (ttt180) cc_final: 0.8376 (tpp80) REVERT: H 62 GLU cc_start: 0.8389 (mp0) cc_final: 0.7673 (mp0) REVERT: H 63 GLU cc_start: 0.8808 (pt0) cc_final: 0.8058 (pm20) REVERT: H 66 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7718 (tm-30) REVERT: H 70 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.8820 (ttpp) REVERT: H 72 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8232 (mp0) REVERT: H 84 ILE cc_start: 0.9400 (mt) cc_final: 0.8926 (pp) REVERT: I 13 MET cc_start: 0.8181 (tmm) cc_final: 0.7918 (tmm) REVERT: I 18 ASP cc_start: 0.8865 (m-30) cc_final: 0.8499 (m-30) REVERT: I 30 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8208 (tmm) REVERT: I 34 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8478 (tpp80) REVERT: I 72 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8350 (mp0) REVERT: I 80 LYS cc_start: 0.8896 (tttt) cc_final: 0.8515 (tttm) REVERT: I 99 ASP cc_start: 0.8877 (t0) cc_final: 0.8397 (t70) REVERT: I 100 SER cc_start: 0.8801 (t) cc_final: 0.8517 (p) REVERT: I 104 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7831 (ttm110) REVERT: J 13 MET cc_start: 0.8464 (tmm) cc_final: 0.8127 (tmm) REVERT: J 15 LYS cc_start: 0.8641 (mttt) cc_final: 0.7944 (ttmm) REVERT: J 21 ARG cc_start: 0.8422 (mmm160) cc_final: 0.8199 (mmm160) REVERT: J 30 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8117 (mmm) REVERT: J 34 ARG cc_start: 0.8653 (ttt180) cc_final: 0.8288 (ttt-90) REVERT: J 35 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8405 (mttm) REVERT: J 66 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7648 (tm-30) REVERT: J 84 ILE cc_start: 0.9349 (mt) cc_final: 0.8885 (pp) REVERT: J 100 SER cc_start: 0.8910 (t) cc_final: 0.8542 (p) REVERT: K 13 MET cc_start: 0.8242 (tmm) cc_final: 0.7949 (tmm) REVERT: K 15 LYS cc_start: 0.8557 (mttt) cc_final: 0.7942 (mtpm) REVERT: K 21 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8328 (mtp85) REVERT: K 26 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8926 (mp) REVERT: K 62 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7930 (mp0) REVERT: K 66 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8190 (tm-30) REVERT: K 76 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7948 (mptt) REVERT: K 80 LYS cc_start: 0.8887 (tttt) cc_final: 0.8502 (tttm) REVERT: K 99 ASP cc_start: 0.8469 (t0) cc_final: 0.8057 (t70) REVERT: K 118 THR cc_start: 0.9188 (m) cc_final: 0.8672 (p) outliers start: 29 outliers final: 18 residues processed: 344 average time/residue: 1.4480 time to fit residues: 521.3162 Evaluate side-chains 352 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 26 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain D residue 58 LEU 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 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 82 LEU 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 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: 0.9980 chunk 88 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 90 optimal weight: 0.0670 chunk 2 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.074298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.055289 restraints weight = 16874.698| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.70 r_work: 0.3393 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8096 Z= 0.267 Angle : 0.899 10.778 11000 Z= 0.453 Chirality : 0.052 0.153 1287 Planarity : 0.007 0.089 1353 Dihedral : 5.668 25.772 1089 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.03 % Allowed : 32.52 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (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 B 31 PHE 0.023 0.001 PHE K 64 TYR 0.023 0.002 TYR K 105 ARG 0.020 0.002 ARG F 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8136.99 seconds wall clock time: 144 minutes 4.46 seconds (8644.46 seconds total)