Starting phenix.real_space_refine on Tue Sep 24 09:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_10150.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_10150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_10150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_10150.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sdz_10150/09_2024/6sdz_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-5461/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: 5.10, per 1000 atoms: 0.64 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 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: 1.70 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: 2.56 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1351 1.32 - 1.44: 2140 1.44 - 1.57: 4559 1.57 - 1.69: 2 1.69 - 1.81: 44 Bond restraints: 8096 Sorted by residual: bond pdb=" CE1 HIS A 31 " pdb=" NE2 HIS A 31 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" CA SER B 112 " pdb=" CB SER B 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER D 112 " pdb=" CB SER D 112 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" CA SER G 112 " pdb=" CB SER G 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.62e+00 bond pdb=" CA SER H 112 " pdb=" CB SER H 112 " ideal model delta sigma weight residual 1.529 1.492 0.037 1.20e-02 6.94e+03 9.47e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10111 1.95 - 3.91: 825 3.91 - 5.86: 59 5.86 - 7.82: 3 7.82 - 9.77: 2 Bond angle restraints: 11000 Sorted by residual: angle pdb=" CD1 LEU G 58 " pdb=" CG LEU G 58 " pdb=" CD2 LEU G 58 " ideal model delta sigma weight residual 110.80 101.03 9.77 2.20e+00 2.07e-01 1.97e+01 angle pdb=" CD1 LEU I 58 " pdb=" CG LEU I 58 " pdb=" CD2 LEU I 58 " ideal model delta sigma weight residual 110.80 102.17 8.63 2.20e+00 2.07e-01 1.54e+01 angle pdb=" O ILE C 68 " pdb=" C ILE C 68 " pdb=" N TYR C 69 " ideal model delta sigma weight residual 121.83 125.46 -3.63 1.03e+00 9.43e-01 1.24e+01 angle pdb=" CA GLU G 62 " pdb=" C GLU G 62 " pdb=" O GLU G 62 " ideal model delta sigma weight residual 121.40 117.46 3.94 1.13e+00 7.83e-01 1.22e+01 angle pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " pdb=" CD GLU H 61 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.70e+00 3.46e-01 1.19e+01 ... (remaining 10995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.00: 4047 11.00 - 21.99: 486 21.99 - 32.99: 172 32.99 - 43.98: 70 43.98 - 54.98: 10 Dihedral angle restraints: 4785 sinusoidal: 1826 harmonic: 2959 Sorted by residual: dihedral pdb=" C GLU E 63 " pdb=" N GLU E 63 " pdb=" CA GLU E 63 " pdb=" CB GLU E 63 " ideal model delta harmonic sigma weight residual -122.60 -131.36 8.76 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" CA ILE K 26 " pdb=" C ILE K 26 " pdb=" N ASN K 27 " pdb=" CA ASN K 27 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE H 26 " pdb=" C ILE H 26 " pdb=" N ASN H 27 " pdb=" CA ASN H 27 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 846 0.076 - 0.151: 364 0.151 - 0.227: 52 0.227 - 0.303: 20 0.303 - 0.379: 5 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CG LEU G 58 " pdb=" CB LEU G 58 " pdb=" CD1 LEU G 58 " pdb=" CD2 LEU G 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CB VAL K 16 " pdb=" CA VAL K 16 " pdb=" CG1 VAL K 16 " pdb=" CG2 VAL K 16 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 1284 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 64 " 0.013 2.00e-02 2.50e+03 4.88e-02 4.16e+01 pdb=" CG PHE K 64 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE K 64 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE K 64 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE K 64 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE K 64 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE K 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " -0.022 2.00e-02 2.50e+03 4.16e-02 3.47e+01 pdb=" CG TYR A 114 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " -0.091 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 114 " -0.019 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR J 114 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR J 114 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR J 114 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR J 114 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 114 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR J 114 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR J 114 " -0.048 2.00e-02 2.50e+03 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1654 2.79 - 3.32: 7696 3.32 - 3.85: 14998 3.85 - 4.37: 17613 4.37 - 4.90: 32309 Nonbonded interactions: 74270 Sorted by model distance: nonbonded pdb=" N SER J 112 " pdb=" OG SER K 112 " model vdw 2.263 3.120 nonbonded pdb=" N SER A 112 " pdb=" OG SER B 112 " model vdw 2.271 3.120 nonbonded pdb=" N SER I 112 " pdb=" OG SER J 112 " model vdw 2.274 3.120 nonbonded pdb=" N SER E 112 " pdb=" OG SER F 112 " model vdw 2.280 3.120 nonbonded pdb=" N SER B 112 " pdb=" OG SER C 112 " model vdw 2.312 3.120 ... (remaining 74265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:17.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 0.937 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: 1.2480 time to fit residues: 516.0863 Evaluate side-chains 336 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8942 (mttt) cc_final: 0.8421 (mtpm) REVERT: A 18 ASP cc_start: 0.8488 (m-30) cc_final: 0.8129 (m-30) REVERT: A 34 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8156 (tpp80) REVERT: A 63 GLU cc_start: 0.8704 (pt0) cc_final: 0.8156 (pp20) REVERT: A 66 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 88 HIS cc_start: 0.8912 (t-90) cc_final: 0.8694 (t-90) REVERT: A 104 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.8089 (mtt-85) REVERT: B 13 MET cc_start: 0.8364 (tmm) cc_final: 0.8116 (tmm) REVERT: B 15 LYS cc_start: 0.8911 (mttt) cc_final: 0.8462 (mtpp) REVERT: B 21 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7773 (tpp80) REVERT: B 34 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8170 (tpp80) REVERT: B 66 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 80 LYS cc_start: 0.9240 (ttpt) cc_final: 0.9017 (ttpt) REVERT: B 90 HIS cc_start: 0.8362 (m90) cc_final: 0.8067 (m90) REVERT: C 63 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: C 66 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: C 90 HIS cc_start: 0.8498 (m90) cc_final: 0.8289 (m90) REVERT: D 13 MET cc_start: 0.8361 (tmm) cc_final: 0.7918 (tmm) REVERT: D 15 LYS cc_start: 0.8761 (mttt) cc_final: 0.8153 (mtpm) REVERT: D 18 ASP cc_start: 0.8504 (m-30) cc_final: 0.8252 (m-30) REVERT: D 34 ARG cc_start: 0.8730 (ttt180) cc_final: 0.8400 (tpp80) REVERT: D 63 GLU cc_start: 0.8313 (pm20) cc_final: 0.8109 (pm20) REVERT: D 69 TYR cc_start: 0.8227 (m-80) cc_final: 0.7991 (m-80) REVERT: E 13 MET cc_start: 0.8576 (tmm) cc_final: 0.7842 (tmm) REVERT: E 15 LYS cc_start: 0.8991 (mttt) cc_final: 0.8527 (mttm) REVERT: E 34 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8423 (tpp80) REVERT: E 66 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7871 (tm-30) REVERT: E 104 ARG cc_start: 0.8356 (ttm110) cc_final: 0.7901 (mtm-85) REVERT: F 13 MET cc_start: 0.8200 (tmm) cc_final: 0.7800 (tmm) REVERT: F 15 LYS cc_start: 0.8809 (mttt) cc_final: 0.8375 (mtpm) REVERT: F 63 GLU cc_start: 0.8174 (pm20) cc_final: 0.7433 (pm20) REVERT: G 13 MET cc_start: 0.8583 (tmm) cc_final: 0.8106 (tmm) REVERT: G 15 LYS cc_start: 0.8958 (mttt) cc_final: 0.8515 (mttm) REVERT: G 34 ARG cc_start: 0.8705 (ttt180) cc_final: 0.8343 (tpp80) REVERT: G 63 GLU cc_start: 0.8500 (pt0) cc_final: 0.8100 (pm20) REVERT: G 104 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8119 (ttm110) REVERT: H 15 LYS cc_start: 0.9017 (mttt) cc_final: 0.8503 (mtpp) REVERT: H 34 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8432 (tpp80) REVERT: H 62 GLU cc_start: 0.8356 (mp0) cc_final: 0.8107 (mp0) REVERT: H 63 GLU cc_start: 0.8657 (pt0) cc_final: 0.8263 (pm20) REVERT: I 15 LYS cc_start: 0.8916 (mttt) cc_final: 0.8353 (mtpp) REVERT: I 18 ASP cc_start: 0.8880 (m-30) cc_final: 0.8668 (m-30) REVERT: I 62 GLU cc_start: 0.8557 (mp0) cc_final: 0.8350 (mp0) REVERT: I 63 GLU cc_start: 0.8568 (pt0) cc_final: 0.8341 (pt0) REVERT: I 80 LYS cc_start: 0.9151 (tttt) cc_final: 0.8941 (tttp) REVERT: I 104 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7907 (ttm110) REVERT: J 13 MET cc_start: 0.8735 (tmm) cc_final: 0.8485 (tmm) REVERT: J 15 LYS cc_start: 0.8826 (mttt) cc_final: 0.8362 (ttmm) REVERT: J 34 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8062 (tpp80) REVERT: J 63 GLU cc_start: 0.8663 (pt0) cc_final: 0.8181 (pt0) REVERT: J 84 ILE cc_start: 0.9471 (mt) cc_final: 0.9098 (pp) REVERT: K 15 LYS cc_start: 0.9078 (mttt) cc_final: 0.8640 (mtpm) REVERT: K 62 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8502 (mp0) REVERT: K 63 GLU cc_start: 0.8666 (pt0) cc_final: 0.8387 (pt0) REVERT: K 80 LYS cc_start: 0.9028 (tttt) cc_final: 0.8784 (tttp) REVERT: K 90 HIS cc_start: 0.8645 (m90) cc_final: 0.8374 (m90) REVERT: K 100 SER cc_start: 0.8273 (t) cc_final: 0.8001 (p) outliers start: 36 outliers final: 6 residues processed: 381 average time/residue: 1.3237 time to fit residues: 530.4923 Evaluate side-chains 348 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 340 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 I residue 82 LEU 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 49 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 90 optimal weight: 0.0020 chunk 97 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8096 Z= 0.350 Angle : 0.780 8.802 11000 Z= 0.401 Chirality : 0.052 0.143 1287 Planarity : 0.005 0.055 1353 Dihedral : 5.873 24.134 1089 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.31 % Allowed : 22.61 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.006 0.002 HIS C 88 PHE 0.026 0.002 PHE K 64 TYR 0.020 0.002 TYR K 105 ARG 0.014 0.002 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 382 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 345 time to evaluate : 0.835 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: 0.8654 (ttt180) cc_final: 0.8228 (tpp80) REVERT: A 62 GLU cc_start: 0.8121 (mp0) cc_final: 0.7903 (mp0) REVERT: A 63 GLU cc_start: 0.8722 (pt0) cc_final: 0.8130 (pp20) REVERT: A 66 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 89 GLU cc_start: 0.8178 (pm20) cc_final: 0.7674 (pm20) REVERT: B 15 LYS cc_start: 0.8977 (mttt) cc_final: 0.8367 (mtpp) REVERT: B 18 ASP cc_start: 0.8674 (m-30) cc_final: 0.7791 (m-30) REVERT: B 34 ARG cc_start: 0.8591 (ttt180) cc_final: 0.8117 (tpp80) REVERT: B 62 GLU cc_start: 0.8435 (mp0) cc_final: 0.8132 (mp0) REVERT: B 66 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 80 LYS cc_start: 0.9274 (ttpt) cc_final: 0.9053 (ttpt) REVERT: B 90 HIS cc_start: 0.8299 (m90) cc_final: 0.8078 (m90) REVERT: B 104 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8262 (mtm-85) REVERT: C 13 MET cc_start: 0.8455 (tmm) cc_final: 0.8182 (tmm) REVERT: C 15 LYS cc_start: 0.8954 (mttt) cc_final: 0.8652 (mtpm) REVERT: C 18 ASP cc_start: 0.8580 (m-30) cc_final: 0.8092 (m-30) REVERT: C 63 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: C 66 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 90 HIS cc_start: 0.8537 (m90) cc_final: 0.8317 (m90) REVERT: C 104 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8113 (ttm110) REVERT: D 13 MET cc_start: 0.8417 (tmm) cc_final: 0.8076 (tmm) REVERT: D 15 LYS cc_start: 0.8832 (mttt) cc_final: 0.8273 (mtpm) REVERT: D 18 ASP cc_start: 0.8522 (m-30) cc_final: 0.8226 (m-30) REVERT: D 34 ARG cc_start: 0.8767 (ttt180) cc_final: 0.8452 (tpp80) REVERT: D 104 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: E 34 ARG cc_start: 0.8707 (ttt180) cc_final: 0.8453 (tpp80) REVERT: E 66 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7987 (tm-30) REVERT: E 104 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8155 (ttm110) REVERT: F 13 MET cc_start: 0.8315 (tmm) cc_final: 0.7941 (tmm) REVERT: F 15 LYS cc_start: 0.8903 (mttt) cc_final: 0.8477 (mtpm) REVERT: F 18 ASP cc_start: 0.8780 (m-30) cc_final: 0.8510 (m-30) REVERT: F 34 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8512 (tpp80) REVERT: F 35 LYS cc_start: 0.9279 (ttpt) cc_final: 0.9078 (ttmm) REVERT: F 63 GLU cc_start: 0.8243 (pm20) cc_final: 0.7673 (pm20) REVERT: F 84 ILE cc_start: 0.9539 (mm) cc_final: 0.9299 (pp) REVERT: G 13 MET cc_start: 0.8703 (tmm) cc_final: 0.8224 (tmm) REVERT: G 15 LYS cc_start: 0.9029 (mttt) cc_final: 0.8371 (mttm) REVERT: G 34 ARG cc_start: 0.8667 (ttt180) cc_final: 0.8317 (tpp80) REVERT: G 63 GLU cc_start: 0.8521 (pt0) cc_final: 0.8112 (pm20) REVERT: G 104 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8141 (ttm110) REVERT: H 15 LYS cc_start: 0.8912 (mttt) cc_final: 0.8601 (mtpt) REVERT: H 34 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8373 (tpp80) REVERT: H 62 GLU cc_start: 0.8515 (mp0) cc_final: 0.7874 (mp0) REVERT: H 63 GLU cc_start: 0.8675 (pt0) cc_final: 0.8338 (pm20) REVERT: H 70 LYS cc_start: 0.9377 (tppp) cc_final: 0.9082 (ttpp) REVERT: I 13 MET cc_start: 0.8443 (tmm) cc_final: 0.7379 (tmm) REVERT: I 15 LYS cc_start: 0.8963 (mttt) cc_final: 0.8566 (mttm) REVERT: I 30 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: I 63 GLU cc_start: 0.8615 (pt0) cc_final: 0.8391 (pt0) REVERT: I 80 LYS cc_start: 0.9172 (tttt) cc_final: 0.8961 (tttm) REVERT: I 104 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7958 (ttm110) REVERT: J 13 MET cc_start: 0.8796 (tmm) cc_final: 0.8551 (tmm) REVERT: J 15 LYS cc_start: 0.8853 (mttt) cc_final: 0.8421 (ttmm) REVERT: J 34 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8136 (tpp80) REVERT: J 63 GLU cc_start: 0.8738 (pt0) cc_final: 0.8276 (pt0) REVERT: J 84 ILE cc_start: 0.9456 (mt) cc_final: 0.9123 (pp) REVERT: K 13 MET cc_start: 0.8717 (tmm) cc_final: 0.8339 (tmt) REVERT: K 15 LYS cc_start: 0.9064 (mttt) cc_final: 0.8648 (mtpm) REVERT: K 63 GLU cc_start: 0.8692 (pt0) cc_final: 0.8425 (pt0) REVERT: K 80 LYS cc_start: 0.9030 (tttt) cc_final: 0.8777 (tttm) REVERT: K 90 HIS cc_start: 0.8711 (m90) cc_final: 0.8465 (m90) REVERT: K 100 SER cc_start: 0.8212 (t) cc_final: 0.7938 (p) outliers start: 37 outliers final: 15 residues processed: 359 average time/residue: 1.3676 time to fit residues: 514.4125 Evaluate side-chains 342 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain K residue 58 LEU 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 88 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 8096 Z= 0.587 Angle : 0.852 9.153 11000 Z= 0.445 Chirality : 0.054 0.165 1287 Planarity : 0.006 0.049 1353 Dihedral : 6.061 25.807 1089 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.18 % Allowed : 23.66 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 79 HIS 0.007 0.002 HIS C 88 PHE 0.026 0.002 PHE K 64 TYR 0.020 0.003 TYR I 116 ARG 0.014 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 382 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 329 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8878 (mttt) cc_final: 0.8463 (mtpm) REVERT: A 18 ASP cc_start: 0.8656 (m-30) cc_final: 0.8186 (m-30) REVERT: A 34 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8339 (tpp80) REVERT: A 62 GLU cc_start: 0.8158 (mp0) cc_final: 0.7861 (mp0) REVERT: A 63 GLU cc_start: 0.8722 (pt0) cc_final: 0.8162 (pp20) REVERT: A 66 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 89 GLU cc_start: 0.8289 (pm20) cc_final: 0.7384 (pm20) REVERT: A 104 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: B 13 MET cc_start: 0.8475 (tmm) cc_final: 0.8169 (tmm) REVERT: B 15 LYS cc_start: 0.8989 (mttt) cc_final: 0.8487 (mtpm) REVERT: B 21 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7773 (tpp80) REVERT: B 34 ARG cc_start: 0.8694 (ttt180) cc_final: 0.8280 (tpp80) REVERT: B 35 LYS cc_start: 0.9154 (ttmt) cc_final: 0.8934 (mtpp) REVERT: B 62 GLU cc_start: 0.8363 (mp0) cc_final: 0.7923 (mp0) REVERT: B 66 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7838 (tm-30) REVERT: B 80 LYS cc_start: 0.9304 (ttpt) cc_final: 0.9095 (ttpt) REVERT: B 104 ARG cc_start: 0.8554 (ttm110) cc_final: 0.7912 (mtm-85) REVERT: C 13 MET cc_start: 0.8529 (tmm) cc_final: 0.8309 (tmm) REVERT: C 15 LYS cc_start: 0.9052 (mttt) cc_final: 0.8683 (mtpm) REVERT: C 18 ASP cc_start: 0.8660 (m-30) cc_final: 0.8072 (m-30) REVERT: C 63 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: C 66 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: C 90 HIS cc_start: 0.8629 (m90) cc_final: 0.8392 (m90) REVERT: D 13 MET cc_start: 0.8533 (tmm) cc_final: 0.8115 (tmm) REVERT: D 15 LYS cc_start: 0.8956 (mttt) cc_final: 0.8397 (mtpm) REVERT: D 18 ASP cc_start: 0.8601 (m-30) cc_final: 0.8336 (m-30) REVERT: D 34 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8426 (tpp80) REVERT: D 62 GLU cc_start: 0.8650 (mp0) cc_final: 0.8424 (mp0) REVERT: D 96 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 104 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8232 (ttm110) REVERT: E 34 ARG cc_start: 0.8748 (ttt180) cc_final: 0.8449 (tpp80) REVERT: E 66 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8028 (tm-30) REVERT: F 13 MET cc_start: 0.8469 (tmm) cc_final: 0.8250 (tmm) REVERT: F 15 LYS cc_start: 0.9017 (mttt) cc_final: 0.8541 (mtpm) REVERT: F 18 ASP cc_start: 0.8744 (m-30) cc_final: 0.8429 (m-30) REVERT: F 35 LYS cc_start: 0.9287 (ttpt) cc_final: 0.9064 (ttmm) REVERT: F 62 GLU cc_start: 0.8698 (pm20) cc_final: 0.8487 (pm20) REVERT: F 63 GLU cc_start: 0.8247 (pm20) cc_final: 0.7696 (pm20) REVERT: G 13 MET cc_start: 0.8793 (tmm) cc_final: 0.8275 (tmm) REVERT: G 15 LYS cc_start: 0.9070 (mttt) cc_final: 0.8438 (mttp) REVERT: G 30 MET cc_start: 0.7515 (tmm) cc_final: 0.5116 (tmm) REVERT: G 34 ARG cc_start: 0.8727 (ttt180) cc_final: 0.8356 (tpp80) REVERT: G 63 GLU cc_start: 0.8622 (pt0) cc_final: 0.8182 (pm20) REVERT: G 89 GLU cc_start: 0.8408 (mp0) cc_final: 0.8146 (mp0) REVERT: G 104 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8176 (ttm110) REVERT: H 15 LYS cc_start: 0.8983 (mttt) cc_final: 0.8654 (mtmt) REVERT: H 34 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8389 (tpp80) REVERT: H 61 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8594 (mt-10) REVERT: H 62 GLU cc_start: 0.8542 (mp0) cc_final: 0.8198 (mp0) REVERT: H 63 GLU cc_start: 0.8723 (pt0) cc_final: 0.8345 (pm20) REVERT: I 13 MET cc_start: 0.8565 (tmm) cc_final: 0.8043 (tmm) REVERT: I 15 LYS cc_start: 0.9034 (mttt) cc_final: 0.8511 (ttmm) REVERT: I 35 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8909 (ttmm) REVERT: I 63 GLU cc_start: 0.8655 (pt0) cc_final: 0.8417 (pt0) REVERT: I 70 LYS cc_start: 0.9419 (ttmm) cc_final: 0.9193 (ttpp) REVERT: I 80 LYS cc_start: 0.9187 (tttt) cc_final: 0.8974 (tttm) REVERT: I 104 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.8055 (ttm110) REVERT: J 34 ARG cc_start: 0.8630 (ttt180) cc_final: 0.8301 (ttt-90) REVERT: J 35 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8789 (mtpt) REVERT: J 58 LEU cc_start: 0.9507 (mt) cc_final: 0.9185 (mt) REVERT: J 61 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: J 63 GLU cc_start: 0.8751 (pt0) cc_final: 0.8260 (pt0) REVERT: J 84 ILE cc_start: 0.9490 (mt) cc_final: 0.9191 (pp) REVERT: K 13 MET cc_start: 0.8729 (tmm) cc_final: 0.8521 (tmm) REVERT: K 15 LYS cc_start: 0.9087 (mttt) cc_final: 0.8641 (mtpm) REVERT: K 62 GLU cc_start: 0.8317 (mp0) cc_final: 0.8027 (mp0) REVERT: K 63 GLU cc_start: 0.8711 (pt0) cc_final: 0.8434 (pt0) REVERT: K 73 ILE cc_start: 0.9202 (mt) cc_final: 0.8893 (mp) REVERT: K 80 LYS cc_start: 0.9046 (tttt) cc_final: 0.8809 (tttm) REVERT: K 90 HIS cc_start: 0.8672 (m90) cc_final: 0.8281 (m90) outliers start: 53 outliers final: 24 residues processed: 352 average time/residue: 1.3857 time to fit residues: 510.8084 Evaluate side-chains 339 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 311 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain 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 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8096 Z= 0.236 Angle : 0.812 9.600 11000 Z= 0.408 Chirality : 0.052 0.169 1287 Planarity : 0.005 0.048 1353 Dihedral : 5.810 24.819 1089 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.66 % Allowed : 26.69 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 79 HIS 0.004 0.001 HIS A 88 PHE 0.029 0.001 PHE K 64 TYR 0.024 0.002 TYR E 105 ARG 0.015 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 395 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 355 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8668 (ttt180) cc_final: 0.8304 (tpp80) REVERT: A 61 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 62 GLU cc_start: 0.8035 (mp0) cc_final: 0.7674 (mp0) REVERT: A 63 GLU cc_start: 0.8672 (pt0) cc_final: 0.8037 (pp20) REVERT: A 66 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 96 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8848 (p) REVERT: A 104 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: B 13 MET cc_start: 0.8477 (tmm) cc_final: 0.8043 (tmm) REVERT: B 15 LYS cc_start: 0.8959 (mttt) cc_final: 0.8517 (mtpm) REVERT: B 18 ASP cc_start: 0.8638 (m-30) cc_final: 0.8195 (m-30) REVERT: B 34 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8197 (tpp80) REVERT: B 62 GLU cc_start: 0.8322 (mp0) cc_final: 0.7793 (mp0) REVERT: B 66 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 80 LYS cc_start: 0.9273 (ttpt) cc_final: 0.9046 (ttpt) REVERT: B 104 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7863 (mtm-85) REVERT: C 15 LYS cc_start: 0.9025 (mttt) cc_final: 0.8671 (mtpm) REVERT: C 18 ASP cc_start: 0.8534 (m-30) cc_final: 0.8057 (m-30) REVERT: C 63 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7822 (pm20) REVERT: C 66 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8168 (pp20) REVERT: C 90 HIS cc_start: 0.8633 (m90) cc_final: 0.8233 (m90) REVERT: D 13 MET cc_start: 0.8467 (tmm) cc_final: 0.8147 (tmm) REVERT: D 15 LYS cc_start: 0.8831 (mttt) cc_final: 0.8354 (mtpp) REVERT: D 34 ARG cc_start: 0.8746 (ttt180) cc_final: 0.8411 (tpp80) REVERT: D 62 GLU cc_start: 0.8555 (mp0) cc_final: 0.8270 (mp0) REVERT: D 63 GLU cc_start: 0.8342 (pm20) cc_final: 0.8141 (pm20) REVERT: D 104 ARG cc_start: 0.8358 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: E 15 LYS cc_start: 0.9037 (mttt) cc_final: 0.8653 (mttp) REVERT: E 34 ARG cc_start: 0.8691 (ttt180) cc_final: 0.8460 (tpp80) REVERT: E 62 GLU cc_start: 0.8711 (pm20) cc_final: 0.8380 (mp0) REVERT: E 66 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7943 (tm-30) REVERT: E 70 LYS cc_start: 0.9350 (ttpp) cc_final: 0.9140 (ttpp) REVERT: E 104 ARG cc_start: 0.8409 (ttm110) cc_final: 0.8170 (ttm110) REVERT: F 13 MET cc_start: 0.8349 (tmm) cc_final: 0.8142 (tmm) REVERT: F 15 LYS cc_start: 0.8967 (mttt) cc_final: 0.8679 (mtpp) REVERT: F 18 ASP cc_start: 0.8678 (m-30) cc_final: 0.8373 (m-30) REVERT: F 35 LYS cc_start: 0.9257 (ttpt) cc_final: 0.9049 (ttmm) REVERT: F 63 GLU cc_start: 0.8257 (pm20) cc_final: 0.7721 (pm20) REVERT: G 13 MET cc_start: 0.8674 (tmm) cc_final: 0.8226 (tmm) REVERT: G 15 LYS cc_start: 0.9018 (mttt) cc_final: 0.8499 (mttp) REVERT: G 34 ARG cc_start: 0.8690 (ttt180) cc_final: 0.8345 (tpp80) REVERT: G 63 GLU cc_start: 0.8516 (pt0) cc_final: 0.7992 (pm20) REVERT: H 15 LYS cc_start: 0.8961 (mttt) cc_final: 0.8621 (mtmm) REVERT: H 34 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8327 (tpp80) REVERT: H 62 GLU cc_start: 0.8484 (mp0) cc_final: 0.7874 (mp0) REVERT: H 63 GLU cc_start: 0.8714 (pt0) cc_final: 0.8382 (pm20) REVERT: H 84 ILE cc_start: 0.9406 (mt) cc_final: 0.9095 (pp) REVERT: I 13 MET cc_start: 0.8495 (tmm) cc_final: 0.7990 (tmm) REVERT: I 15 LYS cc_start: 0.8949 (mttt) cc_final: 0.8316 (ttmm) REVERT: I 18 ASP cc_start: 0.8803 (m-30) cc_final: 0.7876 (m-30) REVERT: I 66 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7913 (tm-30) REVERT: I 70 LYS cc_start: 0.9325 (ttmm) cc_final: 0.9118 (ttpp) REVERT: I 80 LYS cc_start: 0.9157 (tttt) cc_final: 0.8939 (tttm) REVERT: I 99 ASP cc_start: 0.8506 (t0) cc_final: 0.8258 (t70) REVERT: I 104 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7900 (ttm110) REVERT: J 15 LYS cc_start: 0.8859 (mttt) cc_final: 0.8372 (ttmm) REVERT: J 34 ARG cc_start: 0.8588 (ttt180) cc_final: 0.8281 (ttt-90) REVERT: J 35 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8803 (mtpp) REVERT: J 61 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8285 (mt-10) REVERT: J 63 GLU cc_start: 0.8728 (pt0) cc_final: 0.8436 (pt0) REVERT: J 84 ILE cc_start: 0.9477 (mt) cc_final: 0.9273 (pp) REVERT: K 13 MET cc_start: 0.8749 (tmm) cc_final: 0.8507 (tmm) REVERT: K 15 LYS cc_start: 0.9082 (mttt) cc_final: 0.8671 (mtpm) REVERT: K 62 GLU cc_start: 0.8440 (mp0) cc_final: 0.8136 (mp0) REVERT: K 63 GLU cc_start: 0.8657 (pt0) cc_final: 0.8416 (pt0) REVERT: K 80 LYS cc_start: 0.8937 (tttt) cc_final: 0.8711 (tttm) REVERT: K 106 THR cc_start: 0.9063 (m) cc_final: 0.8779 (p) outliers start: 40 outliers final: 14 residues processed: 373 average time/residue: 1.3098 time to fit residues: 512.6400 Evaluate side-chains 340 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 323 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain E residue 58 LEU 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 96 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 0.0010 chunk 95 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS D 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8096 Z= 0.359 Angle : 0.862 10.867 11000 Z= 0.431 Chirality : 0.052 0.147 1287 Planarity : 0.006 0.055 1353 Dihedral : 5.853 25.752 1089 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.66 % Allowed : 27.86 % Favored : 67.48 % 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: -2.85 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 79 HIS 0.005 0.001 HIS C 88 PHE 0.025 0.002 PHE K 64 TYR 0.020 0.002 TYR A 105 ARG 0.017 0.002 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 331 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8298 (tpp80) REVERT: A 62 GLU cc_start: 0.8050 (mp0) cc_final: 0.7681 (mp0) REVERT: A 63 GLU cc_start: 0.8696 (pt0) cc_final: 0.8036 (pp20) REVERT: A 66 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 104 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.7823 (mtm-85) REVERT: B 13 MET cc_start: 0.8556 (tmm) cc_final: 0.8120 (tmm) REVERT: B 15 LYS cc_start: 0.8952 (mttt) cc_final: 0.8515 (mtpm) REVERT: B 18 ASP cc_start: 0.8677 (m-30) cc_final: 0.8242 (m-30) REVERT: B 21 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7792 (tpp80) REVERT: B 34 ARG cc_start: 0.8654 (ttt180) cc_final: 0.8259 (tpp80) REVERT: B 62 GLU cc_start: 0.8302 (mp0) cc_final: 0.7753 (mp0) REVERT: B 66 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7936 (tm-30) REVERT: B 80 LYS cc_start: 0.9282 (ttpt) cc_final: 0.9063 (ttpt) REVERT: B 104 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7836 (mtm-85) REVERT: C 15 LYS cc_start: 0.9027 (mttt) cc_final: 0.8745 (mtpm) REVERT: C 18 ASP cc_start: 0.8551 (m-30) cc_final: 0.7954 (m-30) REVERT: C 63 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: C 66 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8224 (pp20) REVERT: C 90 HIS cc_start: 0.8648 (m90) cc_final: 0.8264 (m90) REVERT: D 13 MET cc_start: 0.8476 (tmm) cc_final: 0.8119 (tmm) REVERT: D 15 LYS cc_start: 0.8872 (mttt) cc_final: 0.8323 (mtpm) REVERT: D 18 ASP cc_start: 0.8529 (m-30) cc_final: 0.8256 (m-30) REVERT: D 34 ARG cc_start: 0.8763 (ttt180) cc_final: 0.8360 (tpp80) REVERT: D 62 GLU cc_start: 0.8581 (mp0) cc_final: 0.8025 (mp0) REVERT: D 66 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 104 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8195 (ttm110) REVERT: E 15 LYS cc_start: 0.9031 (mttt) cc_final: 0.8633 (mttp) REVERT: E 34 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8401 (tpp80) REVERT: E 62 GLU cc_start: 0.8698 (pm20) cc_final: 0.8174 (mp0) REVERT: E 66 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8037 (tm-30) REVERT: F 15 LYS cc_start: 0.9002 (mttt) cc_final: 0.8505 (mtpm) REVERT: F 18 ASP cc_start: 0.8711 (m-30) cc_final: 0.8277 (m-30) REVERT: F 35 LYS cc_start: 0.9274 (ttpt) cc_final: 0.9050 (ttmm) REVERT: F 62 GLU cc_start: 0.8631 (pm20) cc_final: 0.8249 (pm20) REVERT: F 63 GLU cc_start: 0.8289 (pm20) cc_final: 0.7599 (pm20) REVERT: G 13 MET cc_start: 0.8690 (tmm) cc_final: 0.8188 (tmm) REVERT: G 15 LYS cc_start: 0.9041 (mttt) cc_final: 0.8427 (mttp) REVERT: G 34 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8363 (tpp80) REVERT: G 63 GLU cc_start: 0.8578 (pt0) cc_final: 0.8032 (pm20) REVERT: G 72 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8180 (mt-10) REVERT: H 15 LYS cc_start: 0.8943 (mttt) cc_final: 0.8655 (mtmt) REVERT: H 34 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8369 (tpp80) REVERT: H 62 GLU cc_start: 0.8564 (mp0) cc_final: 0.8129 (mp0) REVERT: H 63 GLU cc_start: 0.8745 (pt0) cc_final: 0.8459 (pm20) REVERT: H 84 ILE cc_start: 0.9417 (mt) cc_final: 0.9109 (pp) REVERT: I 13 MET cc_start: 0.8622 (tmm) cc_final: 0.7544 (tmm) REVERT: I 15 LYS cc_start: 0.9008 (mttt) cc_final: 0.8579 (mttm) REVERT: I 18 ASP cc_start: 0.8661 (m-30) cc_final: 0.8304 (m-30) REVERT: I 62 GLU cc_start: 0.8613 (mp0) cc_final: 0.8382 (mp0) REVERT: I 70 LYS cc_start: 0.9314 (ttmm) cc_final: 0.9027 (tppp) REVERT: I 80 LYS cc_start: 0.9170 (tttt) cc_final: 0.8949 (tttm) REVERT: I 104 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7918 (ttm110) REVERT: J 13 MET cc_start: 0.8410 (tmm) cc_final: 0.7205 (tmm) REVERT: J 15 LYS cc_start: 0.8929 (mttt) cc_final: 0.8308 (mtmm) REVERT: J 18 ASP cc_start: 0.8909 (m-30) cc_final: 0.8506 (m-30) REVERT: J 21 ARG cc_start: 0.8472 (mmm160) cc_final: 0.7948 (mmm-85) REVERT: J 30 MET cc_start: 0.7495 (tmm) cc_final: 0.6569 (tmm) REVERT: J 34 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8266 (ttt-90) REVERT: J 63 GLU cc_start: 0.8766 (pt0) cc_final: 0.8457 (pt0) REVERT: J 84 ILE cc_start: 0.9472 (mt) cc_final: 0.9251 (pp) REVERT: K 15 LYS cc_start: 0.9128 (mttt) cc_final: 0.8661 (mtpm) REVERT: K 62 GLU cc_start: 0.8541 (mp0) cc_final: 0.8242 (mp0) REVERT: K 63 GLU cc_start: 0.8677 (pt0) cc_final: 0.8443 (pt0) REVERT: K 80 LYS cc_start: 0.8956 (tttt) cc_final: 0.8728 (tttm) REVERT: K 106 THR cc_start: 0.9095 (m) cc_final: 0.8809 (p) outliers start: 40 outliers final: 15 residues processed: 352 average time/residue: 1.3779 time to fit residues: 507.8104 Evaluate side-chains 343 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 326 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 63 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS H 90 HIS K 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8096 Z= 0.308 Angle : 0.889 10.054 11000 Z= 0.440 Chirality : 0.053 0.241 1287 Planarity : 0.006 0.052 1353 Dihedral : 5.809 25.066 1089 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.85 % Allowed : 29.84 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (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 0.002 0.001 TRP J 79 HIS 0.004 0.001 HIS E 31 PHE 0.027 0.001 PHE K 64 TYR 0.018 0.002 TYR E 105 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 371 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 338 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8254 (tpp80) REVERT: A 62 GLU cc_start: 0.8057 (mp0) cc_final: 0.7691 (mp0) REVERT: A 63 GLU cc_start: 0.8688 (pt0) cc_final: 0.7975 (pp20) REVERT: A 66 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 104 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: B 13 MET cc_start: 0.8524 (tmm) cc_final: 0.7812 (tmm) REVERT: B 15 LYS cc_start: 0.8940 (mttt) cc_final: 0.8466 (mtpm) REVERT: B 18 ASP cc_start: 0.8652 (m-30) cc_final: 0.8222 (m-30) REVERT: B 21 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7799 (tpp80) REVERT: B 34 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8291 (tpp80) REVERT: B 62 GLU cc_start: 0.8303 (mp0) cc_final: 0.7752 (mp0) REVERT: B 66 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7930 (tm-30) REVERT: B 80 LYS cc_start: 0.9271 (ttpt) cc_final: 0.9051 (ttpt) REVERT: B 89 GLU cc_start: 0.8400 (mp0) cc_final: 0.8193 (mp0) REVERT: B 104 ARG cc_start: 0.8444 (ttm110) cc_final: 0.7857 (mtm-85) REVERT: C 15 LYS cc_start: 0.9021 (mttt) cc_final: 0.8754 (mtpm) REVERT: C 18 ASP cc_start: 0.8540 (m-30) cc_final: 0.8033 (m-30) REVERT: C 62 GLU cc_start: 0.8346 (mp0) cc_final: 0.8010 (mp0) REVERT: C 63 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: C 90 HIS cc_start: 0.8613 (m90) cc_final: 0.8358 (m90) REVERT: D 13 MET cc_start: 0.8460 (tmm) cc_final: 0.8218 (tmm) REVERT: D 15 LYS cc_start: 0.8840 (mttt) cc_final: 0.8349 (mtpp) REVERT: D 34 ARG cc_start: 0.8743 (ttt180) cc_final: 0.8288 (tpp80) REVERT: D 58 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8941 (tp) REVERT: D 62 GLU cc_start: 0.8567 (mp0) cc_final: 0.7858 (mp0) REVERT: E 15 LYS cc_start: 0.9015 (mttt) cc_final: 0.8736 (mtpm) REVERT: E 34 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8444 (tpp80) REVERT: E 62 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: E 66 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 15 LYS cc_start: 0.8950 (mttt) cc_final: 0.8578 (mtpm) REVERT: F 18 ASP cc_start: 0.8678 (m-30) cc_final: 0.8280 (m-30) REVERT: F 30 MET cc_start: 0.8021 (tpp) cc_final: 0.7621 (tpp) REVERT: F 35 LYS cc_start: 0.9275 (ttpt) cc_final: 0.9050 (ttmm) REVERT: F 63 GLU cc_start: 0.8264 (pm20) cc_final: 0.7533 (pm20) REVERT: G 13 MET cc_start: 0.8673 (tmm) cc_final: 0.7999 (tmm) REVERT: G 15 LYS cc_start: 0.9021 (mttt) cc_final: 0.8517 (mttp) REVERT: G 34 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8356 (tpp80) REVERT: G 63 GLU cc_start: 0.8541 (pt0) cc_final: 0.7961 (pm20) REVERT: G 70 LYS cc_start: 0.9309 (ttpp) cc_final: 0.8965 (ttpp) REVERT: G 104 ARG cc_start: 0.8431 (ttm110) cc_final: 0.8018 (mtm-85) REVERT: H 34 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8358 (tpp80) REVERT: H 62 GLU cc_start: 0.8520 (mp0) cc_final: 0.8196 (mp0) REVERT: H 63 GLU cc_start: 0.8713 (pt0) cc_final: 0.8387 (pm20) REVERT: H 70 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9084 (ttpp) REVERT: H 84 ILE cc_start: 0.9404 (mt) cc_final: 0.9082 (pp) REVERT: I 13 MET cc_start: 0.8634 (tmm) cc_final: 0.7373 (tmm) REVERT: I 15 LYS cc_start: 0.8959 (mttt) cc_final: 0.8502 (mtmm) REVERT: I 18 ASP cc_start: 0.8641 (m-30) cc_final: 0.8327 (m-30) REVERT: I 62 GLU cc_start: 0.8526 (mp0) cc_final: 0.8285 (mp0) REVERT: I 70 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8922 (tppp) REVERT: I 80 LYS cc_start: 0.9154 (tttt) cc_final: 0.8936 (tttm) REVERT: I 104 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7890 (ttm110) REVERT: J 13 MET cc_start: 0.8454 (tmm) cc_final: 0.7111 (tmm) REVERT: J 15 LYS cc_start: 0.8964 (mttt) cc_final: 0.8442 (mtmm) REVERT: J 30 MET cc_start: 0.7606 (tmm) cc_final: 0.6624 (tmm) REVERT: J 34 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8350 (ttt-90) REVERT: J 35 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8789 (ttmm) REVERT: J 63 GLU cc_start: 0.8742 (pt0) cc_final: 0.8488 (pt0) REVERT: J 84 ILE cc_start: 0.9471 (mt) cc_final: 0.9266 (pp) REVERT: K 15 LYS cc_start: 0.9086 (mttt) cc_final: 0.8706 (mtpm) REVERT: K 62 GLU cc_start: 0.8568 (mp0) cc_final: 0.8216 (mp0) REVERT: K 63 GLU cc_start: 0.8655 (pt0) cc_final: 0.8429 (pt0) REVERT: K 73 ILE cc_start: 0.9081 (mt) cc_final: 0.8820 (mp) REVERT: K 80 LYS cc_start: 0.8917 (tttt) cc_final: 0.8693 (tttm) REVERT: K 106 THR cc_start: 0.9073 (m) cc_final: 0.8805 (p) outliers start: 33 outliers final: 17 residues processed: 355 average time/residue: 1.3644 time to fit residues: 507.4550 Evaluate side-chains 344 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 322 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain 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 70 LYS 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 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 56 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.0060 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 0.0870 chunk 83 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS D 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8096 Z= 0.278 Angle : 0.941 10.498 11000 Z= 0.462 Chirality : 0.053 0.182 1287 Planarity : 0.007 0.075 1353 Dihedral : 5.734 23.409 1089 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.73 % Allowed : 31.82 % 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: -2.99 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 79 HIS 0.003 0.001 HIS B 31 PHE 0.029 0.001 PHE K 64 TYR 0.018 0.002 TYR E 116 ARG 0.019 0.003 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 382 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 350 time to evaluate : 0.935 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 13 MET cc_start: 0.8792 (tpp) cc_final: 0.8325 (tpp) REVERT: A 34 ARG cc_start: 0.8627 (ttt180) cc_final: 0.8232 (tpp80) REVERT: A 61 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 62 GLU cc_start: 0.7965 (mp0) cc_final: 0.7648 (mp0) REVERT: A 63 GLU cc_start: 0.8688 (pt0) cc_final: 0.7981 (pp20) REVERT: A 66 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 96 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8808 (p) REVERT: A 104 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7758 (mtm-85) REVERT: B 15 LYS cc_start: 0.8979 (mttt) cc_final: 0.8513 (mtpm) REVERT: B 18 ASP cc_start: 0.8638 (m-30) cc_final: 0.8152 (m-30) REVERT: B 34 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8282 (tpp80) REVERT: B 62 GLU cc_start: 0.8275 (mp0) cc_final: 0.7836 (mp0) REVERT: B 66 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 80 LYS cc_start: 0.9237 (ttpt) cc_final: 0.9008 (ttpt) REVERT: B 104 ARG cc_start: 0.8385 (ttm110) cc_final: 0.7733 (mtm-85) REVERT: C 15 LYS cc_start: 0.9012 (mttt) cc_final: 0.8797 (mtpt) REVERT: C 18 ASP cc_start: 0.8526 (m-30) cc_final: 0.8266 (m-30) REVERT: C 62 GLU cc_start: 0.8257 (mp0) cc_final: 0.7874 (mp0) REVERT: C 63 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: C 90 HIS cc_start: 0.8566 (m90) cc_final: 0.8298 (m90) REVERT: D 13 MET cc_start: 0.8427 (tmm) cc_final: 0.8167 (tmm) REVERT: D 15 LYS cc_start: 0.8822 (mttt) cc_final: 0.8315 (mtpp) REVERT: D 34 ARG cc_start: 0.8735 (ttt180) cc_final: 0.8276 (tpp80) REVERT: D 58 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8996 (tp) REVERT: D 62 GLU cc_start: 0.8442 (mp0) cc_final: 0.7917 (mp0) REVERT: E 13 MET cc_start: 0.8714 (tmm) cc_final: 0.8398 (tmm) REVERT: E 15 LYS cc_start: 0.8980 (mttt) cc_final: 0.8763 (mtpm) REVERT: E 34 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8357 (tpp80) REVERT: E 62 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: E 66 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7991 (tm-30) REVERT: F 15 LYS cc_start: 0.8891 (mttt) cc_final: 0.8601 (mtpt) REVERT: F 18 ASP cc_start: 0.8687 (m-30) cc_final: 0.8392 (m-30) REVERT: F 30 MET cc_start: 0.7955 (tpp) cc_final: 0.7607 (tpp) REVERT: F 34 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8381 (tpp80) REVERT: F 35 LYS cc_start: 0.9276 (ttpt) cc_final: 0.9025 (ttmm) REVERT: F 62 GLU cc_start: 0.8530 (pm20) cc_final: 0.8276 (mp0) REVERT: F 63 GLU cc_start: 0.8219 (pm20) cc_final: 0.8011 (pm20) REVERT: G 13 MET cc_start: 0.8636 (tmm) cc_final: 0.8050 (tmm) REVERT: G 15 LYS cc_start: 0.9027 (mttt) cc_final: 0.8513 (mttp) REVERT: G 34 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8359 (tpp80) REVERT: G 63 GLU cc_start: 0.8496 (pt0) cc_final: 0.8020 (pm20) REVERT: G 104 ARG cc_start: 0.8404 (ttm110) cc_final: 0.7996 (mtm-85) REVERT: H 34 ARG cc_start: 0.8596 (ttt180) cc_final: 0.8301 (tpp80) REVERT: H 62 GLU cc_start: 0.8469 (mp0) cc_final: 0.7970 (mp0) REVERT: H 63 GLU cc_start: 0.8721 (pt0) cc_final: 0.8384 (pm20) REVERT: H 70 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.9014 (ttpp) REVERT: H 84 ILE cc_start: 0.9396 (mt) cc_final: 0.9075 (pp) REVERT: I 13 MET cc_start: 0.8602 (tmm) cc_final: 0.8314 (tmm) REVERT: I 15 LYS cc_start: 0.8958 (mttt) cc_final: 0.8482 (mtpp) REVERT: I 18 ASP cc_start: 0.8651 (m-30) cc_final: 0.8299 (m-30) REVERT: I 62 GLU cc_start: 0.8456 (mp0) cc_final: 0.8239 (mp0) REVERT: I 70 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8866 (tppp) REVERT: I 80 LYS cc_start: 0.9129 (tttt) cc_final: 0.8913 (tttm) REVERT: I 104 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7854 (ttm110) REVERT: J 13 MET cc_start: 0.8246 (tmm) cc_final: 0.7486 (tmm) REVERT: J 15 LYS cc_start: 0.8939 (mttt) cc_final: 0.8329 (mtmm) REVERT: J 18 ASP cc_start: 0.8787 (m-30) cc_final: 0.8450 (m-30) REVERT: J 21 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7952 (mmm-85) REVERT: J 30 MET cc_start: 0.7589 (tmm) cc_final: 0.6742 (tmm) REVERT: J 34 ARG cc_start: 0.8609 (ttt180) cc_final: 0.8239 (tpp80) REVERT: J 35 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8516 (mttm) REVERT: J 61 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8448 (mt-10) REVERT: J 62 GLU cc_start: 0.8582 (mp0) cc_final: 0.8378 (mp0) REVERT: J 63 GLU cc_start: 0.8741 (pt0) cc_final: 0.8376 (pt0) REVERT: K 15 LYS cc_start: 0.9014 (mttt) cc_final: 0.8711 (mtpm) REVERT: K 62 GLU cc_start: 0.8526 (mp0) cc_final: 0.8140 (mp0) REVERT: K 63 GLU cc_start: 0.8638 (pt0) cc_final: 0.8412 (pt0) REVERT: K 73 ILE cc_start: 0.9041 (mt) cc_final: 0.8758 (mp) REVERT: K 80 LYS cc_start: 0.8866 (tttt) cc_final: 0.8638 (tttm) REVERT: K 106 THR cc_start: 0.9043 (m) cc_final: 0.8820 (p) outliers start: 32 outliers final: 18 residues processed: 366 average time/residue: 1.3255 time to fit residues: 509.0614 Evaluate side-chains 355 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR 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 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain 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 34 ARG Chi-restraints excluded: chain I residue 70 LYS 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 60 THR Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS H 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8096 Z= 0.343 Angle : 0.990 11.637 11000 Z= 0.492 Chirality : 0.054 0.194 1287 Planarity : 0.007 0.076 1353 Dihedral : 5.846 25.029 1089 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.38 % Allowed : 33.22 % Favored : 63.40 % 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: -3.03 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (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 K 88 PHE 0.028 0.002 PHE K 64 TYR 0.021 0.002 TYR E 116 ARG 0.019 0.003 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 360 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8810 (tpp) cc_final: 0.8376 (tpp) REVERT: A 34 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8238 (tpp80) REVERT: A 61 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7708 (mt-10) REVERT: A 62 GLU cc_start: 0.7986 (mp0) cc_final: 0.7744 (mp0) REVERT: A 63 GLU cc_start: 0.8695 (pt0) cc_final: 0.7871 (pp20) REVERT: A 66 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8251 (tm-30) REVERT: A 96 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 15 LYS cc_start: 0.8966 (mttt) cc_final: 0.8563 (mtpm) REVERT: B 34 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8282 (tpp80) REVERT: B 62 GLU cc_start: 0.8310 (mp0) cc_final: 0.7814 (mp0) REVERT: B 63 GLU cc_start: 0.8314 (pm20) cc_final: 0.7837 (pm20) REVERT: B 66 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 80 LYS cc_start: 0.9239 (ttpt) cc_final: 0.9006 (ttpt) REVERT: C 18 ASP cc_start: 0.8469 (m-30) cc_final: 0.7954 (m-30) REVERT: C 63 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: C 90 HIS cc_start: 0.8503 (m90) cc_final: 0.8288 (m90) REVERT: D 13 MET cc_start: 0.8578 (tmm) cc_final: 0.8100 (tmm) REVERT: D 15 LYS cc_start: 0.8859 (mttt) cc_final: 0.8350 (mtpp) REVERT: D 34 ARG cc_start: 0.8742 (ttt180) cc_final: 0.8350 (tpp80) REVERT: D 58 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8928 (tp) REVERT: D 62 GLU cc_start: 0.8282 (mp0) cc_final: 0.7809 (mp0) REVERT: E 15 LYS cc_start: 0.8986 (mttt) cc_final: 0.8461 (mtpm) REVERT: E 34 ARG cc_start: 0.8707 (ttt180) cc_final: 0.8395 (tpp80) REVERT: E 62 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: E 66 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 89 GLU cc_start: 0.8371 (mp0) cc_final: 0.8124 (mp0) REVERT: F 13 MET cc_start: 0.8711 (tmm) cc_final: 0.8422 (tpt) REVERT: F 15 LYS cc_start: 0.8886 (mttt) cc_final: 0.8505 (mtmm) REVERT: F 18 ASP cc_start: 0.8703 (m-30) cc_final: 0.8383 (m-30) REVERT: F 21 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8180 (mmm-85) REVERT: F 35 LYS cc_start: 0.9263 (ttpt) cc_final: 0.9049 (ttmm) REVERT: F 62 GLU cc_start: 0.8529 (pm20) cc_final: 0.8295 (mp0) REVERT: F 63 GLU cc_start: 0.8238 (pm20) cc_final: 0.7989 (pm20) REVERT: G 13 MET cc_start: 0.8620 (tmm) cc_final: 0.7937 (tmm) REVERT: G 15 LYS cc_start: 0.9008 (mttt) cc_final: 0.8524 (mttp) REVERT: G 34 ARG cc_start: 0.8709 (ttt180) cc_final: 0.8348 (tpp80) REVERT: G 63 GLU cc_start: 0.8533 (pt0) cc_final: 0.8099 (pm20) REVERT: G 104 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8221 (ttm-80) REVERT: H 34 ARG cc_start: 0.8617 (ttt180) cc_final: 0.8276 (tpp80) REVERT: H 62 GLU cc_start: 0.8398 (mp0) cc_final: 0.7957 (mp0) REVERT: H 63 GLU cc_start: 0.8756 (pt0) cc_final: 0.8394 (pm20) REVERT: H 84 ILE cc_start: 0.9428 (mt) cc_final: 0.9117 (pp) REVERT: I 13 MET cc_start: 0.8630 (tmm) cc_final: 0.8015 (tmm) REVERT: I 15 LYS cc_start: 0.8984 (mttt) cc_final: 0.8498 (ttmm) REVERT: I 18 ASP cc_start: 0.8663 (m-30) cc_final: 0.8377 (m-30) REVERT: I 62 GLU cc_start: 0.8414 (mp0) cc_final: 0.8214 (mp0) REVERT: I 80 LYS cc_start: 0.9134 (tttt) cc_final: 0.8915 (tttm) REVERT: I 104 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7898 (ttm110) REVERT: J 18 ASP cc_start: 0.8782 (m-30) cc_final: 0.8447 (m-30) REVERT: J 21 ARG cc_start: 0.8461 (mmm160) cc_final: 0.8031 (mmm-85) REVERT: J 30 MET cc_start: 0.7668 (tmm) cc_final: 0.6800 (tmm) REVERT: J 34 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8298 (ttm-80) REVERT: J 35 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8480 (mttm) REVERT: J 61 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8486 (mt-10) REVERT: J 63 GLU cc_start: 0.8750 (pt0) cc_final: 0.8390 (pt0) REVERT: K 62 GLU cc_start: 0.8525 (mp0) cc_final: 0.8196 (mp0) REVERT: K 63 GLU cc_start: 0.8658 (pt0) cc_final: 0.8427 (pt0) REVERT: K 73 ILE cc_start: 0.9052 (mt) cc_final: 0.8775 (mp) REVERT: K 80 LYS cc_start: 0.8872 (tttt) cc_final: 0.8649 (tttm) REVERT: K 106 THR cc_start: 0.9055 (m) cc_final: 0.8794 (p) outliers start: 29 outliers final: 17 residues processed: 345 average time/residue: 1.3534 time to fit residues: 489.1596 Evaluate side-chains 345 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 324 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 34 ARG 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 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 44 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 90 optimal weight: 0.0010 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8096 Z= 0.339 Angle : 1.036 13.662 11000 Z= 0.514 Chirality : 0.053 0.199 1287 Planarity : 0.007 0.081 1353 Dihedral : 5.936 25.181 1089 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.03 % Allowed : 34.27 % Favored : 62.70 % 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: -3.11 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS E 31 PHE 0.031 0.002 PHE K 64 TYR 0.025 0.002 TYR E 116 ARG 0.020 0.003 ARG F 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 336 time to evaluate : 0.981 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 13 MET cc_start: 0.8794 (tpp) cc_final: 0.8311 (tpp) REVERT: A 34 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8234 (tpp80) REVERT: A 61 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 62 GLU cc_start: 0.7957 (mp0) cc_final: 0.7635 (mp0) REVERT: A 63 GLU cc_start: 0.8685 (pt0) cc_final: 0.7982 (pp20) REVERT: A 66 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8215 (tm-30) REVERT: A 96 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8788 (p) REVERT: A 104 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.8129 (mtt90) REVERT: B 15 LYS cc_start: 0.8987 (mttt) cc_final: 0.8559 (mtpm) REVERT: B 34 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8278 (tpp80) REVERT: B 62 GLU cc_start: 0.8351 (mp0) cc_final: 0.7905 (mp0) REVERT: B 66 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7950 (tm-30) REVERT: B 80 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8992 (ttpt) REVERT: C 18 ASP cc_start: 0.8046 (m-30) cc_final: 0.7569 (m-30) REVERT: C 62 GLU cc_start: 0.8375 (mp0) cc_final: 0.8130 (mp0) REVERT: C 63 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: D 13 MET cc_start: 0.8488 (tmm) cc_final: 0.7994 (tmm) REVERT: D 15 LYS cc_start: 0.8834 (mttt) cc_final: 0.8377 (mtpp) REVERT: D 21 ARG cc_start: 0.8154 (mmm160) cc_final: 0.7749 (tpp80) REVERT: D 34 ARG cc_start: 0.8743 (ttt180) cc_final: 0.8345 (tpp80) REVERT: D 58 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8895 (tp) REVERT: D 62 GLU cc_start: 0.8333 (mp0) cc_final: 0.7736 (mp0) REVERT: E 13 MET cc_start: 0.8695 (tmm) cc_final: 0.8342 (tmm) REVERT: E 15 LYS cc_start: 0.8972 (mttt) cc_final: 0.8449 (mtpm) REVERT: E 21 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7775 (mtp85) REVERT: E 34 ARG cc_start: 0.8702 (ttt180) cc_final: 0.8348 (tpp80) REVERT: E 62 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: E 66 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7892 (tm-30) REVERT: F 13 MET cc_start: 0.8712 (tmm) cc_final: 0.8384 (tpt) REVERT: F 15 LYS cc_start: 0.8895 (mttt) cc_final: 0.8455 (mtmm) REVERT: F 18 ASP cc_start: 0.8693 (m-30) cc_final: 0.8376 (m-30) REVERT: F 30 MET cc_start: 0.8037 (tpp) cc_final: 0.7692 (mmm) REVERT: F 35 LYS cc_start: 0.9276 (ttpt) cc_final: 0.9024 (ttmm) REVERT: F 62 GLU cc_start: 0.8530 (pm20) cc_final: 0.8254 (mp0) REVERT: F 63 GLU cc_start: 0.8240 (pm20) cc_final: 0.7943 (pm20) REVERT: G 13 MET cc_start: 0.8621 (tmm) cc_final: 0.8333 (tmm) REVERT: G 15 LYS cc_start: 0.8953 (mttt) cc_final: 0.8474 (mtpp) REVERT: G 34 ARG cc_start: 0.8705 (ttt180) cc_final: 0.8322 (tpp80) REVERT: G 63 GLU cc_start: 0.8479 (pt0) cc_final: 0.8094 (pm20) REVERT: G 104 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8214 (ttm-80) REVERT: H 34 ARG cc_start: 0.8644 (ttt180) cc_final: 0.8353 (tpp80) REVERT: H 35 LYS cc_start: 0.8937 (mttm) cc_final: 0.8587 (mptp) REVERT: H 62 GLU cc_start: 0.8409 (mp0) cc_final: 0.7965 (mp0) REVERT: H 63 GLU cc_start: 0.8782 (pt0) cc_final: 0.8374 (pm20) REVERT: H 72 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8386 (mt-10) REVERT: I 13 MET cc_start: 0.8622 (tmm) cc_final: 0.8063 (tmm) REVERT: I 15 LYS cc_start: 0.9000 (mttt) cc_final: 0.8490 (ttmm) REVERT: I 18 ASP cc_start: 0.8686 (m-30) cc_final: 0.8313 (m-30) REVERT: I 62 GLU cc_start: 0.8396 (mp0) cc_final: 0.8193 (mp0) REVERT: I 80 LYS cc_start: 0.9127 (tttt) cc_final: 0.8905 (tttm) REVERT: I 104 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7896 (ttm110) REVERT: J 15 LYS cc_start: 0.8936 (mttt) cc_final: 0.8672 (mtpp) REVERT: J 18 ASP cc_start: 0.8749 (m-30) cc_final: 0.8477 (m-30) REVERT: J 21 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8049 (mmm-85) REVERT: J 30 MET cc_start: 0.7748 (tmm) cc_final: 0.6863 (tmm) REVERT: J 34 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8286 (ttm-80) REVERT: J 35 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8459 (mttm) REVERT: J 61 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: J 63 GLU cc_start: 0.8745 (pt0) cc_final: 0.8357 (pt0) REVERT: K 62 GLU cc_start: 0.8525 (mp0) cc_final: 0.8199 (mp0) REVERT: K 63 GLU cc_start: 0.8646 (pt0) cc_final: 0.8422 (pt0) REVERT: K 80 LYS cc_start: 0.8866 (tttt) cc_final: 0.8641 (tttm) REVERT: K 106 THR cc_start: 0.9070 (m) cc_final: 0.8809 (p) outliers start: 26 outliers final: 18 residues processed: 348 average time/residue: 1.3788 time to fit residues: 502.8320 Evaluate side-chains 342 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 319 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain K residue 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 72 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS K 27 ASN K 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.072036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.053208 restraints weight = 17076.106| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.63 r_work: 0.3364 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8096 Z= 0.389 Angle : 1.059 14.098 11000 Z= 0.523 Chirality : 0.054 0.202 1287 Planarity : 0.007 0.088 1353 Dihedral : 6.031 25.161 1089 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.80 % Allowed : 35.43 % Favored : 61.77 % 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: -3.16 (0.23), residues: 968 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.008 0.001 HIS B 90 PHE 0.032 0.002 PHE K 64 TYR 0.023 0.003 TYR E 116 ARG 0.021 0.003 ARG K 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6595.56 seconds wall clock time: 114 minutes 50.94 seconds (6890.94 seconds total)