Starting phenix.real_space_refine on Sat Aug 8 23:00:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.map" model { file = "/net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v29_64721/08_2026/9v29_64721.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 966 5.49 5 S 59 5.16 5 C 15478 2.51 5 N 5677 2.21 5 O 8420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30600 Number of models: 1 Model: "" Number of chains: 20 Chain: "sB" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Chain: "sC" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 72 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain breaks: 1 Chain: "sI" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "sJ" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "sK" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "sa" Number of atoms: 19911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 19911 Classifications: {'RNA': 930} Modifications used: {'rna2p_pur': 93, 'rna2p_pyr': 48, 'rna3p_pur': 449, 'rna3p_pyr': 340} Link IDs: {'rna2p': 140, 'rna3p': 789} Chain breaks: 16 Chain: "sb" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 156 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 2, 'TRANS': 17} Chain breaks: 1 Chain: "sc" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1231 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 Chain: "se" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 973 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 8 Chain: "sf" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 7, 'TRANS': 78} Chain breaks: 3 Chain: "sh" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 437 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "si" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 151 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain breaks: 1 Chain: "sj" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 772 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain breaks: 4 Chain: "sk" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 346 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain breaks: 2 Chain: "sm" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1118 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "so" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 604 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 3 Chain: "sp" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "sr" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain breaks: 3 Chain: "sy" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 2 Chain: "sa" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PAR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.18 Number of scatterers: 30600 At special positions: 0 Unit cell: (139.1, 163.71, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 966 15.00 O 8420 8.00 N 5677 7.00 C 15478 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: 2.02 Conformation dependent library (CDL) restraints added in 557.2 milliseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 15 sheets defined 25.2% alpha, 18.1% beta 288 base pairs and 474 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'sB' and resid 49 through 56 Processing helix chain 'sB' and resid 74 through 81 Processing helix chain 'sB' and resid 90 through 94 removed outlier: 3.701A pdb=" N ARGsB 93 " --> pdb=" O THRsB 90 " (cutoff:3.500A) Processing helix chain 'sb' and resid 137 through 145 Processing helix chain 'sc' and resid 67 through 75 removed outlier: 4.286A pdb=" N VALsc 71 " --> pdb=" O GLUsc 67 " (cutoff:3.500A) Processing helix chain 'sc' and resid 122 through 137 removed outlier: 3.564A pdb=" N ILEsc 132 " --> pdb=" O LYSsc 128 " (cutoff:3.500A) Processing helix chain 'sc' and resid 183 through 194 removed outlier: 3.500A pdb=" N PHEsc 189 " --> pdb=" O THRsc 185 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLYsc 194 " --> pdb=" O LEUsc 190 " (cutoff:3.500A) Processing helix chain 'sc' and resid 208 through 222 Processing helix chain 'se' and resid 72 through 77 Processing helix chain 'se' and resid 78 through 82 removed outlier: 3.661A pdb=" N PHEse 81 " --> pdb=" O ASNse 78 " (cutoff:3.500A) Processing helix chain 'se' and resid 108 through 114 Processing helix chain 'se' and resid 159 through 166 removed outlier: 3.764A pdb=" N ILEse 166 " --> pdb=" O GLNse 162 " (cutoff:3.500A) Processing helix chain 'sf' and resid 13 through 17 Processing helix chain 'sh' and resid 175 through 179 removed outlier: 3.716A pdb=" N ASNsh 178 " --> pdb=" O ASPsh 175 " (cutoff:3.500A) Processing helix chain 'si' and resid 123 through 132 removed outlier: 3.619A pdb=" N GLUsi 129 " --> pdb=" O LYSsi 125 " (cutoff:3.500A) Processing helix chain 'sj' and resid 25 through 29 Processing helix chain 'sj' and resid 49 through 51 No H-bonds generated for 'chain 'sj' and resid 49 through 51' Processing helix chain 'sj' and resid 87 through 91 Processing helix chain 'sj' and resid 208 through 213 Processing helix chain 'sk' and resid 20 through 28 removed outlier: 4.088A pdb=" N ALAsk 26 " --> pdb=" O GLUsk 22 " (cutoff:3.500A) Processing helix chain 'sk' and resid 52 through 60 removed outlier: 3.670A pdb=" N METsk 59 " --> pdb=" O ILEsk 55 " (cutoff:3.500A) Processing helix chain 'sm' and resid 44 through 50 removed outlier: 4.116A pdb=" N ILEsm 48 " --> pdb=" O PROsm 44 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYSsm 49 " --> pdb=" O ALAsm 45 " (cutoff:3.500A) Processing helix chain 'so' and resid 87 through 91 Processing helix chain 'so' and resid 95 through 99 Processing helix chain 'so' and resid 101 through 103 No H-bonds generated for 'chain 'so' and resid 101 through 103' Processing helix chain 'so' and resid 108 through 132 removed outlier: 3.588A pdb=" N SERso 131 " --> pdb=" O ARGso 127 " (cutoff:3.500A) Processing helix chain 'sp' and resid 54 through 56 No H-bonds generated for 'chain 'sp' and resid 54 through 56' Processing helix chain 'sp' and resid 59 through 63 Processing helix chain 'sp' and resid 65 through 84 removed outlier: 3.685A pdb=" N ARGsp 79 " --> pdb=" O ASPsp 75 " (cutoff:3.500A) Processing helix chain 'sp' and resid 105 through 117 removed outlier: 4.627A pdb=" N ALAsp 109 " --> pdb=" O PROsp 105 " (cutoff:3.500A) Processing helix chain 'sr' and resid 5 through 20 Processing helix chain 'sr' and resid 33 through 44 removed outlier: 3.816A pdb=" N VALsr 40 " --> pdb=" O GLUsr 36 " (cutoff:3.500A) Processing helix chain 'sr' and resid 85 through 94 Processing helix chain 'sr' and resid 114 through 119 Processing helix chain 'sy' and resid 7 through 20 removed outlier: 4.013A pdb=" N METsy 11 " --> pdb=" O ALAsy 7 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRPsy 20 " --> pdb=" O ARGsy 16 " (cutoff:3.500A) Processing helix chain 'sy' and resid 22 through 28 removed outlier: 3.740A pdb=" N GLYsy 28 " --> pdb=" O GLUsy 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'sB' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'sB' and resid 36 through 43 Processing sheet with id=AA3, first strand: chain 'sc' and resid 81 through 91 removed outlier: 5.173A pdb=" N VALsc 82 " --> pdb=" O ALAsc 105 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALAsc 105 " --> pdb=" O VALsc 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'sc' and resid 160 through 163 Processing sheet with id=AA5, first strand: chain 'se' and resid 29 through 32 Processing sheet with id=AA6, first strand: chain 'se' and resid 67 through 71 removed outlier: 3.576A pdb=" N GLYse 104 " --> pdb=" O LYSse 87 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILEse 214 " --> pdb=" O ILEse 142 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILEse 142 " --> pdb=" O ILEse 214 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSse 216 " --> pdb=" O PHEse 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'sf' and resid 178 through 180 removed outlier: 3.584A pdb=" N GLYsf 191 " --> pdb=" O ALAsf 179 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N HISsf 207 " --> pdb=" O VALsf 194 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'sh' and resid 153 through 154 removed outlier: 3.798A pdb=" N VALsh 205 " --> pdb=" O CYSsh 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'sh' and resid 170 through 174 Processing sheet with id=AB1, first strand: chain 'sj' and resid 44 through 47 Processing sheet with id=AB2, first strand: chain 'sj' and resid 64 through 66 removed outlier: 6.745A pdb=" N ASNsj 64 " --> pdb=" O GLYsj 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'sm' and resid 66 through 76 removed outlier: 17.118A pdb=" N THRsm 69 " --> pdb=" O PHEsm 90 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N PHEsm 90 " --> pdb=" O THRsm 69 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N SERsm 71 " --> pdb=" O ASPsm 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASPsm 88 " --> pdb=" O SERsm 71 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILEsm 84 " --> pdb=" O LYSsm 75 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHEsm 137 " --> pdb=" O ALAsm 107 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VALsm 139 " --> pdb=" O GLYsm 126 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLYsm 126 " --> pdb=" O VALsm 139 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VALsm 123 " --> pdb=" O LEUsm 70 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEUsm 70 " --> pdb=" O VALsm 123 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILEsm 125 " --> pdb=" O ARGsm 68 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ARGsm 68 " --> pdb=" O ILEsm 125 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLNsm 127 " --> pdb=" O ARGsm 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'sp' and resid 47 through 52 removed outlier: 7.028A pdb=" N VALsp 39 " --> pdb=" O ILEsp 48 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARGsp 50 " --> pdb=" O VALsp 37 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VALsp 37 " --> pdb=" O ARGsp 50 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THRsp 52 " --> pdb=" O THRsp 35 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THRsp 35 " --> pdb=" O THRsp 52 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HISsp 38 " --> pdb=" O HISsp 27 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALsp 25 " --> pdb=" O THRsp 40 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEUsp 88 " --> pdb=" O ILEsp 121 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARGsp 123 " --> pdb=" O LEUsp 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'sr' and resid 72 through 74 removed outlier: 6.777A pdb=" N VALsr 103 " --> pdb=" O LEUsr 126 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHEsr 128 " --> pdb=" O ALAsr 101 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALAsr 101 " --> pdb=" O PHEsr 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'sy' and resid 78 through 82 293 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 682 hydrogen bonds 1106 hydrogen bond angles 0 basepair planarities 288 basepair parallelities 474 stacking parallelities Total time for adding SS restraints: 9.01 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4572 1.33 - 1.45: 14101 1.45 - 1.57: 12548 1.57 - 1.70: 1907 1.70 - 1.82: 89 Bond restraints: 33217 Sorted by residual: bond pdb=" O3' Asa 292 " pdb=" P Usa 293 " ideal model delta sigma weight residual 1.607 1.508 0.099 1.20e-02 6.94e+03 6.85e+01 bond pdb=" O3' Asa 291 " pdb=" P Asa 292 " ideal model delta sigma weight residual 1.607 1.513 0.094 1.20e-02 6.94e+03 6.15e+01 bond pdb=" C1' Asa1089 " pdb=" N9 Asa1089 " ideal model delta sigma weight residual 1.483 1.392 0.091 1.50e-02 4.44e+03 3.65e+01 bond pdb=" C5' Csa1090 " pdb=" C4' Csa1090 " ideal model delta sigma weight residual 1.508 1.470 0.038 7.00e-03 2.04e+04 2.99e+01 bond pdb=" O3' Usa 293 " pdb=" P Gsa 294 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.20e-02 6.94e+03 2.61e+01 ... (remaining 33212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 49380 4.09 - 8.18: 91 8.18 - 12.27: 4 12.27 - 16.36: 0 16.36 - 20.45: 1 Bond angle restraints: 49476 Sorted by residual: angle pdb=" O3' Asa 295 " pdb=" C3' Asa 295 " pdb=" C2' Asa 295 " ideal model delta sigma weight residual 113.70 93.25 20.45 1.60e+00 3.91e-01 1.63e+02 angle pdb=" N1 Usa 787 " pdb=" C2 Usa 787 " pdb=" O2 Usa 787 " ideal model delta sigma weight residual 122.80 128.25 -5.45 7.00e-01 2.04e+00 6.06e+01 angle pdb=" C1' Usa 787 " pdb=" N1 Usa 787 " pdb=" C2 Usa 787 " ideal model delta sigma weight residual 117.70 126.88 -9.18 1.20e+00 6.94e-01 5.85e+01 angle pdb=" O2 Usa 787 " pdb=" C2 Usa 787 " pdb=" N3 Usa 787 " ideal model delta sigma weight residual 122.20 117.12 5.08 7.00e-01 2.04e+00 5.26e+01 angle pdb=" N9 Gsa1894 " pdb=" C4 Gsa1894 " pdb=" C5 Gsa1894 " ideal model delta sigma weight residual 105.40 108.17 -2.77 4.00e-01 6.25e+00 4.81e+01 ... (remaining 49471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 18514 35.71 - 71.43: 2043 71.43 - 107.14: 218 107.14 - 142.85: 6 142.85 - 178.56: 12 Dihedral angle restraints: 20793 sinusoidal: 17248 harmonic: 3545 Sorted by residual: dihedral pdb=" CA SERsr 76 " pdb=" C SERsr 76 " pdb=" N PROsr 77 " pdb=" CA PROsr 77 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" O4' Usa 59 " pdb=" C1' Usa 59 " pdb=" N1 Usa 59 " pdb=" C2 Usa 59 " ideal model delta sinusoidal sigma weight residual 200.00 28.08 171.92 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' Csa 980 " pdb=" C1' Csa 980 " pdb=" N1 Csa 980 " pdb=" C2 Csa 980 " ideal model delta sinusoidal sigma weight residual 200.00 30.69 169.31 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 20790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4580 0.051 - 0.102: 759 0.102 - 0.154: 939 0.154 - 0.205: 35 0.205 - 0.256: 7 Chirality restraints: 6320 Sorted by residual: chirality pdb=" C3' Csa1090 " pdb=" C4' Csa1090 " pdb=" O3' Csa1090 " pdb=" C2' Csa1090 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3' Usa1908 " pdb=" C4' Usa1908 " pdb=" O3' Usa1908 " pdb=" C2' Usa1908 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' Asa1089 " pdb=" O4' Asa1089 " pdb=" C2' Asa1089 " pdb=" N9 Asa1089 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 6317 not shown) Planarity restraints: 2647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' Asa 295 " -0.056 2.00e-02 2.50e+03 2.68e-02 1.97e+01 pdb=" N9 Asa 295 " 0.054 2.00e-02 2.50e+03 pdb=" C8 Asa 295 " -0.005 2.00e-02 2.50e+03 pdb=" N7 Asa 295 " 0.014 2.00e-02 2.50e+03 pdb=" C5 Asa 295 " 0.013 2.00e-02 2.50e+03 pdb=" C6 Asa 295 " -0.006 2.00e-02 2.50e+03 pdb=" N6 Asa 295 " -0.035 2.00e-02 2.50e+03 pdb=" N1 Asa 295 " 0.013 2.00e-02 2.50e+03 pdb=" C2 Asa 295 " 0.002 2.00e-02 2.50e+03 pdb=" N3 Asa 295 " 0.004 2.00e-02 2.50e+03 pdb=" C4 Asa 295 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERsr 76 " -0.063 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PROsr 77 " 0.164 5.00e-02 4.00e+02 pdb=" CA PROsr 77 " -0.050 5.00e-02 4.00e+02 pdb=" CD PROsr 77 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' Csa1090 " -0.048 2.00e-02 2.50e+03 2.33e-02 1.22e+01 pdb=" N1 Csa1090 " 0.039 2.00e-02 2.50e+03 pdb=" C2 Csa1090 " 0.004 2.00e-02 2.50e+03 pdb=" O2 Csa1090 " 0.019 2.00e-02 2.50e+03 pdb=" N3 Csa1090 " -0.017 2.00e-02 2.50e+03 pdb=" C4 Csa1090 " -0.007 2.00e-02 2.50e+03 pdb=" N4 Csa1090 " -0.012 2.00e-02 2.50e+03 pdb=" C5 Csa1090 " 0.010 2.00e-02 2.50e+03 pdb=" C6 Csa1090 " 0.011 2.00e-02 2.50e+03 ... (remaining 2644 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 1200 2.65 - 3.21: 25639 3.21 - 3.77: 60392 3.77 - 4.34: 80522 4.34 - 4.90: 107194 Nonbonded interactions: 274947 Sorted by model distance: nonbonded pdb=" N2 Gsa1824 " pdb=" O2 Usa1890 " model vdw 2.083 2.496 nonbonded pdb=" O THRsC 12 " pdb=" OG SERsC 15 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THRsB 2 " pdb=" N SERsB 3 " model vdw 2.101 3.120 nonbonded pdb=" O2' Csa 400 " pdb=" O ARGsh 189 " model vdw 2.108 3.040 nonbonded pdb=" O2' Asa 972 " pdb=" O2 Usa1932 " model vdw 2.112 3.040 ... (remaining 274942 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 1.240 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 29.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 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 : 0.004 0.099 33217 Z= 0.392 Angle : 0.834 20.451 49476 Z= 0.685 Chirality : 0.061 0.256 6320 Planarity : 0.005 0.095 2647 Dihedral : 22.750 178.563 18497 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.41 % Allowed : 26.82 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1160 helix: -1.04 (0.31), residues: 242 sheet: -0.80 (0.34), residues: 238 loop : -1.34 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGsr 78 TYR 0.012 0.001 TYRsc 145 PHE 0.014 0.001 PHEsp 23 TRP 0.009 0.001 TRPsy 20 HIS 0.008 0.001 HISsr 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.39 (33217) covalent geometry : angle 0.83440 / 0.68 (49476) hydrogen bonds : bond 0.17117 / 14.15 ( 975) hydrogen bonds : angle 6.42860 / 4.97 ( 1892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sc 81 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: se 86 TYR cc_start: 0.8806 (m-80) cc_final: 0.8567 (m-80) REVERT: se 197 LYS cc_start: 0.6953 (mptt) cc_final: 0.6560 (mmtt) REVERT: sf 36 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6818 (ttp) REVERT: sh 161 MET cc_start: 0.7769 (mmm) cc_final: 0.7460 (mmm) REVERT: sj 22 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: sj 59 ARG cc_start: 0.5504 (ptt-90) cc_final: 0.4880 (ptt180) REVERT: sj 94 ASN cc_start: 0.5787 (m-40) cc_final: 0.5391 (m-40) REVERT: sp 70 MET cc_start: 0.8309 (ppp) cc_final: 0.8077 (ppp) REVERT: sr 36 GLU cc_start: 0.6591 (tt0) cc_final: 0.5865 (tm-30) REVERT: sr 47 ILE cc_start: 0.8201 (tp) cc_final: 0.7944 (pt) REVERT: sr 112 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7351 (p0) REVERT: sy 103 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5974 (t80) outliers start: 36 outliers final: 14 residues processed: 126 average time/residue: 0.1679 time to fit residues: 34.7669 Evaluate side-chains 101 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sc residue 81 GLU Chi-restraints excluded: chain sf residue 36 MET Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain si residue 105 HIS Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain sp residue 40 THR Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 112 ASP Chi-restraints excluded: chain sy residue 62 SER Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sc 227 GLN se 62 GLN sm 116 GLN sm 138 ASN ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.048347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.044116 restraints weight = 312643.470| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.89 r_work: 0.3554 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 33217 Z= 0.256 Angle : 0.729 10.733 49476 Z= 0.396 Chirality : 0.048 0.472 6320 Planarity : 0.007 0.103 2647 Dihedral : 22.898 178.608 16052 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 7.68 % Allowed : 24.27 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.24), residues: 1160 helix: -0.85 (0.30), residues: 250 sheet: -0.84 (0.35), residues: 235 loop : -1.47 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGsj 56 TYR 0.020 0.002 TYRse 32 PHE 0.028 0.003 PHEsr 37 TRP 0.058 0.004 TRPse 31 HIS 0.010 0.002 HISsr 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.26 (33217) covalent geometry : angle 0.72913 / 0.40 (49476) hydrogen bonds : bond 0.08968 / 6.39 ( 975) hydrogen bonds : angle 4.53170 / 3.69 ( 1892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 96 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sC 16 GLU cc_start: 0.5616 (OUTLIER) cc_final: 0.5356 (mp0) REVERT: sc 79 LYS cc_start: 0.7914 (tmtt) cc_final: 0.7499 (tmtt) REVERT: sc 81 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7091 (tp30) REVERT: sc 131 MET cc_start: 0.8976 (mtt) cc_final: 0.8749 (mtt) REVERT: sc 145 TYR cc_start: 0.8452 (m-80) cc_final: 0.8164 (m-80) REVERT: se 86 TYR cc_start: 0.8932 (m-80) cc_final: 0.8624 (m-80) REVERT: sh 195 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5985 (mmm-85) REVERT: sj 29 MET cc_start: 0.8204 (tpp) cc_final: 0.7955 (tpp) REVERT: sj 95 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (p) REVERT: sm 12 GLN cc_start: 0.5426 (OUTLIER) cc_final: 0.5108 (tt0) REVERT: so 89 TYR cc_start: 0.7973 (t80) cc_final: 0.5981 (m-80) REVERT: sp 23 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7528 (t80) REVERT: sr 36 GLU cc_start: 0.6862 (tt0) cc_final: 0.6507 (tt0) REVERT: sr 47 ILE cc_start: 0.8686 (tp) cc_final: 0.8318 (pt) REVERT: sr 82 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7940 (p) REVERT: sy 46 LYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4811 (tttt) REVERT: sy 100 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7753 (pt) REVERT: sy 103 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6014 (t80) REVERT: sy 106 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.6402 (mtm-85) outliers start: 81 outliers final: 39 residues processed: 162 average time/residue: 0.2136 time to fit residues: 54.9427 Evaluate side-chains 140 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 81 GLU Chi-restraints excluded: chain sc residue 197 ASP Chi-restraints excluded: chain sc residue 202 THR Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 62 GLN Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 182 ILE Chi-restraints excluded: chain sf residue 187 MET Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sh residue 150 THR Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 121 SER Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 95 THR Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain sp residue 23 PHE Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 55 MET Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sr residue 6 VAL Chi-restraints excluded: chain sr residue 82 THR Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 46 LYS Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 54 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 124 optimal weight: 6.9990 chunk 91 optimal weight: 40.0000 chunk 194 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 73 optimal weight: 40.0000 chunk 213 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sB 20 ASN se 47 GLN sh 186 ASN sm 10 GLN sr 39 ASN sr 45 GLN sr 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.048499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.044170 restraints weight = 312069.415| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.89 r_work: 0.3563 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33217 Z= 0.165 Angle : 0.557 7.858 49476 Z= 0.320 Chirality : 0.039 0.441 6320 Planarity : 0.005 0.099 2647 Dihedral : 22.781 178.873 16037 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 6.35 % Allowed : 25.59 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1160 helix: -0.43 (0.31), residues: 255 sheet: -0.71 (0.34), residues: 223 loop : -1.37 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsB 93 TYR 0.034 0.002 TYRsi 131 PHE 0.014 0.001 PHEsr 37 TRP 0.009 0.002 TRPse 31 HIS 0.005 0.001 HISsm 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (33217) covalent geometry : angle 0.55683 / 0.32 (49476) hydrogen bonds : bond 0.07870 / 5.62 ( 975) hydrogen bonds : angle 4.17081 / 3.40 ( 1892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 90 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sc 79 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7506 (tmtt) REVERT: sc 81 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: se 86 TYR cc_start: 0.8893 (m-80) cc_final: 0.8568 (m-80) REVERT: sf 195 LYS cc_start: 0.7764 (pttm) cc_final: 0.7375 (pttm) REVERT: sh 195 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6006 (mmm-85) REVERT: sj 29 MET cc_start: 0.8158 (tpp) cc_final: 0.7919 (tpp) REVERT: sj 59 ARG cc_start: 0.5252 (ptt-90) cc_final: 0.4850 (ptt180) REVERT: sm 10 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.5879 (mm110) REVERT: sm 12 GLN cc_start: 0.5161 (OUTLIER) cc_final: 0.4834 (tt0) REVERT: so 89 TYR cc_start: 0.8015 (t80) cc_final: 0.6031 (m-80) REVERT: sr 36 GLU cc_start: 0.7105 (tt0) cc_final: 0.6652 (tt0) REVERT: sr 47 ILE cc_start: 0.8745 (tp) cc_final: 0.8351 (pt) REVERT: sr 57 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6900 (mtt90) REVERT: sr 98 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6439 (p90) REVERT: sr 112 ASP cc_start: 0.7960 (p0) cc_final: 0.7745 (p0) REVERT: sy 100 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.7866 (pt) REVERT: sy 103 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6025 (t80) REVERT: sy 106 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6433 (mtm-85) outliers start: 67 outliers final: 39 residues processed: 141 average time/residue: 0.1905 time to fit residues: 44.0607 Evaluate side-chains 134 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 81 GLU Chi-restraints excluded: chain sc residue 197 ASP Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 182 ILE Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 194 VAL Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sj residue 20 SER Chi-restraints excluded: chain sj residue 21 MET Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 10 GLN Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 57 ARG Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Chi-restraints excluded: chain sy residue 106 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 145 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 chunk 29 optimal weight: 50.0000 chunk 141 optimal weight: 40.0000 chunk 53 optimal weight: 50.0000 chunk 126 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 163 optimal weight: 8.9990 chunk 134 optimal weight: 0.0270 chunk 49 optimal weight: 50.0000 chunk 165 optimal weight: 2.9990 overall best weight: 12.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sc 211 ASN sf 31 HIS sf 34 HIS ** sh 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** si 128 HIS sm 10 GLN ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sr 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.047844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.043448 restraints weight = 310947.384| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.70 r_work: 0.3546 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 33217 Z= 0.278 Angle : 0.701 9.804 49476 Z= 0.382 Chirality : 0.048 0.517 6320 Planarity : 0.006 0.101 2647 Dihedral : 22.852 179.852 16037 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.33 % Favored : 92.50 % Rotamer: Outliers : 7.87 % Allowed : 24.64 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1160 helix: -0.51 (0.31), residues: 247 sheet: -0.84 (0.34), residues: 235 loop : -1.57 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGsr 28 TYR 0.027 0.003 TYRsm 9 PHE 0.022 0.002 PHEsp 23 TRP 0.014 0.003 TRPsy 20 HIS 0.018 0.002 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.28 (33217) covalent geometry : angle 0.70076 / 0.38 (49476) hydrogen bonds : bond 0.09241 / 6.58 ( 975) hydrogen bonds : angle 4.30595 / 3.54 ( 1892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 91 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sC 16 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5414 (mp0) REVERT: sc 79 LYS cc_start: 0.7870 (tmtt) cc_final: 0.7209 (tmtt) REVERT: sc 81 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: sc 207 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7429 (mmtp) REVERT: se 86 TYR cc_start: 0.8991 (m-80) cc_final: 0.8699 (m-80) REVERT: sf 15 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7872 (p-80) REVERT: sh 160 MET cc_start: 0.7927 (mmp) cc_final: 0.7589 (mmp) REVERT: sh 195 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.5038 (tmm-80) REVERT: si 131 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.4956 (p90) REVERT: sm 12 GLN cc_start: 0.5471 (OUTLIER) cc_final: 0.5202 (tt0) REVERT: sm 88 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7081 (t70) REVERT: sr 98 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6323 (p90) REVERT: sy 100 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8013 (pt) REVERT: sy 103 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6237 (t80) outliers start: 83 outliers final: 55 residues processed: 159 average time/residue: 0.1841 time to fit residues: 47.9352 Evaluate side-chains 151 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 85 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 81 GLU Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 197 ASP Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 182 ILE Chi-restraints excluded: chain sf residue 187 MET Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 129 GLU Chi-restraints excluded: chain si residue 131 TYR Chi-restraints excluded: chain sj residue 20 SER Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 95 THR Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 51 THR Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain so residue 98 VAL Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 69 LEU Chi-restraints excluded: chain sr residue 82 THR Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 24 optimal weight: 50.0000 chunk 72 optimal weight: 40.0000 chunk 102 optimal weight: 40.0000 chunk 12 optimal weight: 50.0000 chunk 177 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 160 optimal weight: 0.0030 chunk 83 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 overall best weight: 5.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sc 222 GLN sr 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.048428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.044042 restraints weight = 312234.491| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.76 r_work: 0.3575 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33217 Z= 0.147 Angle : 0.540 7.892 49476 Z= 0.310 Chirality : 0.038 0.436 6320 Planarity : 0.005 0.100 2647 Dihedral : 22.708 179.382 16037 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 5.97 % Allowed : 27.39 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.24), residues: 1160 helix: -0.24 (0.31), residues: 252 sheet: -0.73 (0.34), residues: 238 loop : -1.41 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsp 112 TYR 0.011 0.001 TYRsc 103 PHE 0.014 0.001 PHEsr 37 TRP 0.013 0.002 TRPsf 16 HIS 0.004 0.001 HISsf 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (33217) covalent geometry : angle 0.54027 / 0.31 (49476) hydrogen bonds : bond 0.07466 / 5.26 ( 975) hydrogen bonds : angle 3.97696 / 3.27 ( 1892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 90 time to evaluate : 0.409 Fit side-chains REVERT: sc 79 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7576 (tmtt) REVERT: sc 212 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.8018 (t80) REVERT: se 86 TYR cc_start: 0.8888 (m-80) cc_final: 0.8522 (m-80) REVERT: sj 22 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7558 (pp30) REVERT: sj 59 ARG cc_start: 0.5120 (ptt-90) cc_final: 0.4765 (ptt180) REVERT: sm 12 GLN cc_start: 0.5282 (OUTLIER) cc_final: 0.4961 (tt0) REVERT: sm 88 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6906 (t70) REVERT: sr 36 GLU cc_start: 0.7303 (tt0) cc_final: 0.6987 (tm-30) REVERT: sr 98 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6225 (p90) REVERT: sr 112 ASP cc_start: 0.7985 (p0) cc_final: 0.7752 (p0) REVERT: sy 100 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7891 (pt) REVERT: sy 103 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6052 (t80) outliers start: 63 outliers final: 42 residues processed: 134 average time/residue: 0.1706 time to fit residues: 37.9918 Evaluate side-chains 136 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 197 ASP Chi-restraints excluded: chain sc residue 212 PHE Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 213 TYR Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 40 LEU Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 194 VAL Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 131 TYR Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 142 optimal weight: 20.0000 chunk 105 optimal weight: 40.0000 chunk 26 optimal weight: 50.0000 chunk 211 optimal weight: 7.9990 chunk 49 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 76 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 overall best weight: 25.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sh 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** sr 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.046983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.042797 restraints weight = 314937.802| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.93 r_work: 0.3512 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 33217 Z= 0.502 Angle : 1.018 11.330 49476 Z= 0.510 Chirality : 0.068 0.626 6320 Planarity : 0.008 0.117 2647 Dihedral : 23.005 179.660 16032 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.02 % Favored : 91.81 % Rotamer: Outliers : 7.96 % Allowed : 26.92 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.23), residues: 1160 helix: -0.95 (0.30), residues: 241 sheet: -1.23 (0.34), residues: 235 loop : -1.94 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGsk 53 TYR 0.027 0.004 TYRsm 96 PHE 0.023 0.003 PHEsp 23 TRP 0.021 0.004 TRPsf 16 HIS 0.014 0.003 HISsb 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.50 (33217) covalent geometry : angle 1.01843 / 0.51 (49476) hydrogen bonds : bond 0.11705 / 8.31 ( 975) hydrogen bonds : angle 4.71291 / 3.95 ( 1892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 79 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: sc 207 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7370 (mmtp) REVERT: sf 104 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6290 (mtpp) REVERT: sh 160 MET cc_start: 0.8124 (mmp) cc_final: 0.7771 (mmp) REVERT: sh 195 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6425 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: sj 59 ARG cc_start: 0.5383 (ptt-90) cc_final: 0.4635 (ptt-90) REVERT: sk 3 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6882 (mmt90) REVERT: sm 12 GLN cc_start: 0.5631 (OUTLIER) cc_final: 0.4983 (mt0) REVERT: sm 88 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7191 (t70) REVERT: sr 98 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6601 (p90) REVERT: sy 74 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5260 (pttt) REVERT: sy 100 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8073 (pt) REVERT: sy 103 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6417 (t80) outliers start: 84 outliers final: 60 residues processed: 145 average time/residue: 0.1959 time to fit residues: 45.6342 Evaluate side-chains 147 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 76 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 202 THR Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 40 LEU Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 182 ILE Chi-restraints excluded: chain sf residue 187 MET Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 194 VAL Chi-restraints excluded: chain sf residue 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 129 GLU Chi-restraints excluded: chain si residue 131 TYR Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 21 MET Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 95 THR Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 3 ARG Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 51 THR Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 4 MET Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain so residue 98 VAL Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 86 THR Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 69 LEU Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sr residue 125 ILE Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 74 LYS Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 4 optimal weight: 4.9990 chunk 89 optimal weight: 40.0000 chunk 167 optimal weight: 10.0000 chunk 10 optimal weight: 50.0000 chunk 208 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 55 optimal weight: 50.0000 chunk 127 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 30 optimal weight: 50.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sr 44 HIS ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.048114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.043766 restraints weight = 311585.965| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.74 r_work: 0.3564 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33217 Z= 0.172 Angle : 0.596 9.197 49476 Z= 0.337 Chirality : 0.041 0.482 6320 Planarity : 0.005 0.103 2647 Dihedral : 22.811 179.272 16032 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.48 % Rotamer: Outliers : 6.35 % Allowed : 28.53 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.24), residues: 1160 helix: -0.56 (0.30), residues: 258 sheet: -0.84 (0.34), residues: 230 loop : -1.61 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGsp 141 TYR 0.014 0.002 TYRsi 131 PHE 0.015 0.001 PHEse 207 TRP 0.010 0.002 TRPse 31 HIS 0.006 0.001 HISsm 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (33217) covalent geometry : angle 0.59637 / 0.34 (49476) hydrogen bonds : bond 0.08039 / 5.69 ( 975) hydrogen bonds : angle 4.05822 / 3.35 ( 1892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 89 time to evaluate : 0.625 Fit side-chains REVERT: se 79 GLU cc_start: 0.8499 (tp30) cc_final: 0.7495 (tp30) REVERT: se 86 TYR cc_start: 0.8883 (m-80) cc_final: 0.8617 (m-80) REVERT: se 197 LYS cc_start: 0.6825 (mptt) cc_final: 0.6597 (mmtt) REVERT: sh 195 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6683 (mmm-85) REVERT: sj 22 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7591 (pp30) REVERT: sj 59 ARG cc_start: 0.5086 (ptt-90) cc_final: 0.4735 (ptt180) REVERT: sm 12 GLN cc_start: 0.5330 (OUTLIER) cc_final: 0.4963 (tt0) REVERT: sm 88 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7252 (t70) REVERT: sp 23 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7599 (t80) REVERT: sp 119 MET cc_start: 0.8668 (mmm) cc_final: 0.7588 (mmm) REVERT: sr 57 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7096 (mtt90) REVERT: sr 98 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.6027 (p90) REVERT: sy 100 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8295 (pt) REVERT: sy 103 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6195 (t80) outliers start: 67 outliers final: 43 residues processed: 137 average time/residue: 0.1820 time to fit residues: 40.8937 Evaluate side-chains 137 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 85 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 67 THR Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 194 VAL Chi-restraints excluded: chain sf residue 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sh residue 160 MET Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 131 TYR Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 59 PHE Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain so residue 4 MET Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain sp residue 23 PHE Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sr residue 57 ARG Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 194 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 55 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 117 optimal weight: 6.9990 chunk 209 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sf 207 HIS sr 45 GLN sr 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.048557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.044149 restraints weight = 311772.144| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.81 r_work: 0.3581 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 33217 Z= 0.131 Angle : 0.527 10.549 49476 Z= 0.302 Chirality : 0.037 0.407 6320 Planarity : 0.005 0.100 2647 Dihedral : 22.572 178.534 16032 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 5.69 % Allowed : 29.38 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.24), residues: 1160 helix: -0.01 (0.32), residues: 251 sheet: -0.61 (0.36), residues: 217 loop : -1.36 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsi 122 TYR 0.014 0.001 TYRsi 131 PHE 0.021 0.001 PHEsr 37 TRP 0.010 0.002 TRPsf 16 HIS 0.020 0.001 HISsr 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (33217) covalent geometry : angle 0.52667 / 0.30 (49476) hydrogen bonds : bond 0.07128 / 5.00 ( 975) hydrogen bonds : angle 3.89697 / 3.25 ( 1892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 89 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: se 79 GLU cc_start: 0.8415 (tp30) cc_final: 0.7398 (tp30) REVERT: se 86 TYR cc_start: 0.8855 (m-80) cc_final: 0.8619 (m-80) REVERT: sj 22 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7573 (pp30) REVERT: sj 59 ARG cc_start: 0.4975 (ptt-90) cc_final: 0.4612 (ptt180) REVERT: sm 12 GLN cc_start: 0.5259 (OUTLIER) cc_final: 0.4965 (tt0) REVERT: sm 88 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6959 (t70) REVERT: sp 23 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7616 (t80) REVERT: sr 36 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6916 (tm-30) REVERT: sr 57 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7184 (mtt90) REVERT: sr 98 HIS cc_start: 0.7312 (OUTLIER) cc_final: 0.6223 (p90) REVERT: sy 103 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6182 (t80) outliers start: 60 outliers final: 42 residues processed: 131 average time/residue: 0.1781 time to fit residues: 38.9115 Evaluate side-chains 137 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 88 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sh residue 203 ILE Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain sm residue 125 ILE Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain sp residue 23 PHE Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 45 GLN Chi-restraints excluded: chain sr residue 57 ARG Chi-restraints excluded: chain sr residue 69 LEU Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 126 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 177 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 187 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 92 optimal weight: 40.0000 chunk 99 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sf 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** sm 16 HIS sr 44 HIS ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sr 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.047916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.043507 restraints weight = 311351.093| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.82 r_work: 0.3551 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33217 Z= 0.248 Angle : 0.664 16.353 49476 Z= 0.357 Chirality : 0.045 0.514 6320 Planarity : 0.006 0.107 2647 Dihedral : 22.629 178.758 16030 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 5.59 % Allowed : 29.38 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.24), residues: 1160 helix: -0.32 (0.31), residues: 251 sheet: -0.85 (0.35), residues: 233 loop : -1.49 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsk 53 TYR 0.017 0.002 TYRsm 96 PHE 0.016 0.002 PHEsp 23 TRP 0.012 0.002 TRPsy 20 HIS 0.007 0.001 HISsb 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.25 (33217) covalent geometry : angle 0.66381 / 0.36 (49476) hydrogen bonds : bond 0.08193 / 5.77 ( 975) hydrogen bonds : angle 4.05822 / 3.38 ( 1892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 84 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: se 79 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: sj 22 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7628 (pp30) REVERT: sj 59 ARG cc_start: 0.5057 (ptt-90) cc_final: 0.4393 (ptt-90) REVERT: sm 12 GLN cc_start: 0.5356 (OUTLIER) cc_final: 0.4974 (tt0) REVERT: sm 39 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6959 (ptp) REVERT: sm 88 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7072 (t70) REVERT: sp 23 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7604 (t80) REVERT: sr 36 GLU cc_start: 0.7709 (tt0) cc_final: 0.7367 (tm-30) REVERT: sr 57 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7087 (mtt90) REVERT: sr 98 HIS cc_start: 0.7280 (OUTLIER) cc_final: 0.6092 (p90) REVERT: sy 100 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8003 (pt) REVERT: sy 103 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6228 (t80) outliers start: 59 outliers final: 47 residues processed: 128 average time/residue: 0.1781 time to fit residues: 37.9927 Evaluate side-chains 139 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 187 MET Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 194 VAL Chi-restraints excluded: chain sf residue 204 GLU Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sh residue 203 ILE Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 102 ILE Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain sm residue 125 ILE Chi-restraints excluded: chain so residue 4 MET Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain sp residue 23 PHE Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 57 ARG Chi-restraints excluded: chain sr residue 69 LEU Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 62 SER Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 136 optimal weight: 0.0170 chunk 31 optimal weight: 60.0000 chunk 105 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 170 optimal weight: 10.0000 chunk 26 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 overall best weight: 9.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sf 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** sr 44 HIS sr 45 GLN sr 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.047989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.043619 restraints weight = 309527.874| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.72 r_work: 0.3558 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33217 Z= 0.212 Angle : 0.619 14.439 49476 Z= 0.340 Chirality : 0.043 0.501 6320 Planarity : 0.005 0.106 2647 Dihedral : 22.663 179.271 16030 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 5.69 % Allowed : 29.67 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.24), residues: 1160 helix: -0.32 (0.31), residues: 250 sheet: -0.80 (0.35), residues: 227 loop : -1.50 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGsr 78 TYR 0.012 0.002 TYRsm 96 PHE 0.016 0.002 PHEsp 23 TRP 0.011 0.002 TRPsy 20 HIS 0.006 0.001 HISsr 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.21 (33217) covalent geometry : angle 0.61930 / 0.34 (49476) hydrogen bonds : bond 0.07902 / 5.57 ( 975) hydrogen bonds : angle 4.02457 / 3.33 ( 1892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 82 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: sc 67 GLU cc_start: 0.8257 (pm20) cc_final: 0.8007 (pm20) REVERT: sc 79 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7111 (tmtt) REVERT: sc 207 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7279 (mmtp) REVERT: se 79 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: sh 195 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.5477 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7611 (pp30) REVERT: sj 59 ARG cc_start: 0.5042 (ptt-90) cc_final: 0.4376 (ptt-90) REVERT: sm 12 GLN cc_start: 0.5327 (OUTLIER) cc_final: 0.4949 (tt0) REVERT: sm 88 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7244 (t70) REVERT: sr 36 GLU cc_start: 0.7646 (tt0) cc_final: 0.7303 (tm-30) REVERT: sr 57 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7200 (mtt90) REVERT: sr 98 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6000 (p90) REVERT: sy 100 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8252 (pt) REVERT: sy 103 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6239 (t80) outliers start: 60 outliers final: 46 residues processed: 130 average time/residue: 0.1848 time to fit residues: 39.5867 Evaluate side-chains 138 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 82 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sB residue 2 THR Chi-restraints excluded: chain sB residue 56 ASN Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 40 LEU Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 187 MET Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 204 GLU Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sh residue 203 ILE Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 71 SER Chi-restraints excluded: chain sm residue 79 MET Chi-restraints excluded: chain sm residue 88 ASP Chi-restraints excluded: chain sm residue 123 VAL Chi-restraints excluded: chain sm residue 125 ILE Chi-restraints excluded: chain so residue 4 MET Chi-restraints excluded: chain so residue 16 ILE Chi-restraints excluded: chain so residue 96 VAL Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 45 GLN Chi-restraints excluded: chain sr residue 57 ARG Chi-restraints excluded: chain sr residue 69 LEU Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 62 SER Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 140 optimal weight: 0.0970 chunk 35 optimal weight: 50.0000 chunk 43 optimal weight: 50.0000 chunk 154 optimal weight: 8.9990 chunk 29 optimal weight: 50.0000 chunk 13 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sf 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** sr 44 HIS sr 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.047791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.043447 restraints weight = 311030.902| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.71 r_work: 0.3557 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 33217 Z= 0.219 Angle : 0.743 59.164 49476 Z= 0.428 Chirality : 0.044 0.933 6320 Planarity : 0.006 0.151 2647 Dihedral : 22.663 179.269 16030 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 5.78 % Allowed : 29.29 % Favored : 64.93 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1160 helix: -0.32 (0.31), residues: 250 sheet: -0.80 (0.35), residues: 227 loop : -1.48 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsk 53 TYR 0.012 0.002 TYRsm 96 PHE 0.076 0.002 PHEsp 23 TRP 0.010 0.002 TRPsy 20 HIS 0.035 0.002 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.22 (33217) covalent geometry : angle 0.74292 / 0.43 (49476) hydrogen bonds : bond 0.07880 / 5.56 ( 975) hydrogen bonds : angle 4.02313 / 3.33 ( 1892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5719.82 seconds wall clock time: 99 minutes 30.51 seconds (5970.51 seconds total)