Starting phenix.real_space_refine on Sun Jul 5 23:07:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v29_64721/07_2026/9v29_64721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v29_64721/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9v29_64721/07_2026/9v29_64721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v29_64721/07_2026/9v29_64721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v29_64721/07_2026/9v29_64721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v29_64721/07_2026/9v29_64721.map" } 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-dev-6108/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: 6.77, per 1000 atoms: 0.22 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: 2.56 Conformation dependent library (CDL) restraints added in 730.8 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: 4.56 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: 9.86 Time building geometry restraints manager: 3.51 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 1.50e-02 4.44e+03 4.38e+01 bond pdb=" O3' Asa 291 " pdb=" P Asa 292 " ideal model delta sigma weight residual 1.607 1.513 0.094 1.50e-02 4.44e+03 3.93e+01 bond pdb=" C1' Asa1089 " pdb=" N9 Asa1089 " ideal model delta sigma weight residual 1.475 1.392 0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" O3' Usa 293 " pdb=" P Gsa 294 " ideal model delta sigma weight residual 1.607 1.546 0.061 1.50e-02 4.44e+03 1.67e+01 bond pdb=" N9 Gsa1846 " pdb=" C4 Gsa1846 " ideal model delta sigma weight residual 1.375 1.401 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 33212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 49378 4.09 - 8.18: 93 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 1.50e+00 4.44e-01 1.86e+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 - 0.068: 5901 0.068 - 0.135: 373 0.135 - 0.203: 39 0.203 - 0.271: 6 0.271 - 0.338: 1 Chirality restraints: 6320 Sorted by residual: chirality pdb=" C2' Asa 292 " pdb=" C3' Asa 292 " pdb=" O2' Asa 292 " pdb=" C1' Asa 292 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.34 2.00e-01 2.50e+01 2.86e+00 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 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 33.950 Find NCS groups from input model: 0.120 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.120 ------------------------------------------------------------------------------- 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= 0.358 Angle : 0.620 20.451 49476 Z= 0.526 Chirality : 0.036 0.338 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 0.00401 / 0.36 (33217) covalent geometry : angle 0.62005 / 0.53 (49476) hydrogen bonds : bond 0.17117 / 13.28 ( 975) hydrogen bonds : angle 6.42860 / 4.89 ( 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 : 0.648 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: 0.5392 (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: 0.1981 time to fit residues: 40.6682 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 : 0.654 ------------------------------------------------------------------------------- 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: 40.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.048256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.043850 restraints weight = 313323.554| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.88 r_work: 0.3562 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33217 Z= 0.266 Angle : 0.664 11.416 49476 Z= 0.383 Chirality : 0.043 0.313 6320 Planarity : 0.007 0.103 2647 Dihedral : 22.949 178.746 16052 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 8.25 % Allowed : 23.60 % Favored : 68.15 % 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: -1.77 (0.24), residues: 1160 helix: -0.79 (0.30), residues: 250 sheet: -0.85 (0.35), residues: 235 loop : -1.45 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGsj 56 TYR 0.020 0.003 TYRse 32 PHE 0.028 0.003 PHEsr 37 TRP 0.050 0.004 TRPse 31 HIS 0.013 0.002 HISsm 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.27 (33217) covalent geometry : angle 0.66441 / 0.38 (49476) hydrogen bonds : bond 0.08660 / 6.07 ( 975) hydrogen bonds : angle 4.48451 / 3.58 ( 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 184 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 97 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sC 16 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: sc 79 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7459 (tmtt) REVERT: sc 81 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7075 (tp30) REVERT: sc 131 MET cc_start: 0.9000 (mtt) cc_final: 0.8777 (mtt) REVERT: sc 145 TYR cc_start: 0.8465 (m-80) cc_final: 0.8181 (m-80) REVERT: sc 172 VAL cc_start: 0.9021 (OUTLIER) cc_final: 0.8768 (t) REVERT: se 86 TYR cc_start: 0.8958 (m-80) cc_final: 0.8639 (m-80) REVERT: sf 204 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: sh 195 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5976 (mmm-85) REVERT: sj 95 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (p) REVERT: sm 12 GLN cc_start: 0.5325 (OUTLIER) cc_final: 0.5018 (tt0) REVERT: so 89 TYR cc_start: 0.8008 (t80) cc_final: 0.5966 (m-80) REVERT: sp 23 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7554 (t80) REVERT: sr 36 GLU cc_start: 0.6883 (tt0) cc_final: 0.6520 (tt0) REVERT: sr 47 ILE cc_start: 0.8701 (tp) cc_final: 0.8320 (pt) REVERT: sr 82 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7842 (p) REVERT: sy 46 LYS cc_start: 0.4964 (OUTLIER) cc_final: 0.4712 (tttt) REVERT: sy 100 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7711 (pt) REVERT: sy 103 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6002 (t80) REVERT: sy 106 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6369 (mtm-85) outliers start: 87 outliers final: 38 residues processed: 168 average time/residue: 0.2125 time to fit residues: 56.3411 Evaluate side-chains 143 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 92 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 65 ILE 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 202 THR Chi-restraints excluded: chain se residue 49 VAL 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 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 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 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: 0.7980 chunk 91 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 73 optimal weight: 40.0000 chunk 213 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sB 20 ASN se 47 GLN se 62 GLN sh 186 ASN sr 39 ASN sr 44 HIS sr 45 GLN sr 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.048572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.044165 restraints weight = 313484.149| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.72 r_work: 0.3579 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33217 Z= 0.154 Angle : 0.499 9.949 49476 Z= 0.299 Chirality : 0.036 0.276 6320 Planarity : 0.005 0.099 2647 Dihedral : 22.849 179.220 16037 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 5.78 % Allowed : 25.97 % Favored : 68.25 % 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: -1.42 (0.24), residues: 1160 helix: -0.27 (0.30), residues: 257 sheet: -0.66 (0.34), residues: 224 loop : -1.32 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGsf 196 TYR 0.018 0.002 TYRsi 131 PHE 0.019 0.001 PHEse 26 TRP 0.008 0.002 TRPse 31 HIS 0.005 0.001 HISsm 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (33217) covalent geometry : angle 0.49943 / 0.30 (49476) hydrogen bonds : bond 0.07340 / 5.15 ( 975) hydrogen bonds : angle 4.09047 / 3.30 ( 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 155 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 94 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sc 79 LYS cc_start: 0.7932 (tmtt) cc_final: 0.7613 (tmtt) REVERT: se 86 TYR cc_start: 0.8914 (m-80) cc_final: 0.8592 (m-80) REVERT: sf 195 LYS cc_start: 0.7779 (pttm) cc_final: 0.7562 (pttm) REVERT: sh 195 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6496 (mmm-85) REVERT: sj 59 ARG cc_start: 0.5174 (ptt-90) cc_final: 0.4813 (ptt180) REVERT: sm 12 GLN cc_start: 0.5041 (OUTLIER) cc_final: 0.4660 (tt0) REVERT: so 89 TYR cc_start: 0.7984 (t80) cc_final: 0.5998 (m-80) REVERT: sr 36 GLU cc_start: 0.7061 (tt0) cc_final: 0.6572 (tt0) REVERT: sr 47 ILE cc_start: 0.8778 (tp) cc_final: 0.8404 (pt) REVERT: sr 57 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6845 (mtt90) REVERT: sr 98 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6383 (p90) REVERT: sr 112 ASP cc_start: 0.7854 (p0) cc_final: 0.7609 (p0) REVERT: sy 100 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7827 (pt) REVERT: sy 103 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5994 (t80) REVERT: sy 106 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.6412 (mtm-85) outliers start: 61 outliers final: 36 residues processed: 140 average time/residue: 0.1993 time to fit residues: 45.0572 Evaluate side-chains 130 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 87 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 47 GLN Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 62 GLN Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 190 VAL Chi-restraints excluded: chain sf residue 215 THR 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 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 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: 30.0000 chunk 91 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 141 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 163 optimal weight: 3.9990 chunk 134 optimal weight: 0.0000 chunk 49 optimal weight: 50.0000 chunk 165 optimal weight: 0.5980 overall best weight: 10.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sc 211 ASN sc 222 GLN se 47 GLN sf 31 HIS si 128 HIS sr 44 HIS ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sr 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.047917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.043647 restraints weight = 312123.161| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.99 r_work: 0.3539 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 33217 Z= 0.260 Angle : 0.607 12.318 49476 Z= 0.355 Chirality : 0.041 0.293 6320 Planarity : 0.006 0.100 2647 Dihedral : 22.852 179.949 16034 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.16 % Favored : 92.67 % Rotamer: Outliers : 7.11 % Allowed : 25.50 % Favored : 67.39 % 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: -1.53 (0.24), residues: 1160 helix: -0.33 (0.31), residues: 246 sheet: -0.65 (0.34), residues: 231 loop : -1.43 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGsk 53 TYR 0.016 0.002 TYRsm 96 PHE 0.020 0.002 PHEsp 23 TRP 0.013 0.002 TRPsy 20 HIS 0.018 0.002 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.26 (33217) covalent geometry : angle 0.60701 / 0.36 (49476) hydrogen bonds : bond 0.08457 / 5.94 ( 975) hydrogen bonds : angle 4.19172 / 3.41 ( 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 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 90 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: sC 16 GLU cc_start: 0.5695 (OUTLIER) cc_final: 0.5361 (mp0) REVERT: sc 79 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7193 (tmtt) REVERT: se 86 TYR cc_start: 0.8972 (m-80) cc_final: 0.8643 (m-80) REVERT: sf 15 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7846 (p-80) REVERT: sf 104 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6438 (mtpp) REVERT: sf 180 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7082 (tpt) REVERT: sh 195 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6726 (mmm-85) REVERT: si 131 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.4902 (p90) REVERT: sm 12 GLN cc_start: 0.5405 (OUTLIER) cc_final: 0.5047 (tt0) REVERT: sr 98 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6290 (p90) REVERT: sr 112 ASP cc_start: 0.7928 (p0) cc_final: 0.7708 (p0) REVERT: sy 100 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8010 (pt) REVERT: sy 103 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6227 (t80) REVERT: sy 106 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6551 (mtm-85) outliers start: 75 outliers final: 51 residues processed: 149 average time/residue: 0.2012 time to fit residues: 48.9587 Evaluate side-chains 144 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 82 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 sc residue 70 ILE Chi-restraints excluded: chain sc residue 71 VAL 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 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 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 180 MET 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 24 optimal weight: 50.0000 chunk 72 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 12 optimal weight: 40.0000 chunk 177 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 83 optimal weight: 40.0000 chunk 132 optimal weight: 5.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3822 r_free = 0.3822 target = 0.048246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.043838 restraints weight = 312898.802| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.75 r_work: 0.3565 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33217 Z= 0.177 Angle : 0.513 8.272 49476 Z= 0.307 Chirality : 0.037 0.274 6320 Planarity : 0.005 0.100 2647 Dihedral : 22.782 179.881 16034 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 6.54 % Allowed : 26.64 % Favored : 66.82 % 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: -1.39 (0.24), residues: 1160 helix: -0.14 (0.31), residues: 251 sheet: -0.65 (0.34), residues: 237 loop : -1.34 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGsk 53 TYR 0.011 0.002 TYRso 113 PHE 0.012 0.001 PHEsr 37 TRP 0.010 0.002 TRPsy 20 HIS 0.006 0.001 HISsr 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.18 (33217) covalent geometry : angle 0.51314 / 0.31 (49476) hydrogen bonds : bond 0.07264 / 5.07 ( 975) hydrogen bonds : angle 3.95980 / 3.21 ( 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 158 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 89 time to evaluate : 0.664 Fit side-chains REVERT: sC 16 GLU cc_start: 0.5424 (OUTLIER) cc_final: 0.5158 (mp0) REVERT: sc 79 LYS cc_start: 0.7786 (tmtt) cc_final: 0.7316 (tmtt) REVERT: sc 207 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7348 (mmtp) REVERT: se 86 TYR cc_start: 0.8921 (m-80) cc_final: 0.8586 (m-80) REVERT: sf 180 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6963 (tpt) REVERT: sh 195 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6749 (mmm-85) REVERT: sj 22 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7573 (pp30) REVERT: sm 12 GLN cc_start: 0.5270 (OUTLIER) cc_final: 0.4882 (tt0) REVERT: sr 36 GLU cc_start: 0.7268 (tt0) cc_final: 0.6947 (tm-30) REVERT: sr 98 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6270 (p90) REVERT: sy 100 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7926 (pt) REVERT: sy 103 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6111 (t80) outliers start: 69 outliers final: 47 residues processed: 142 average time/residue: 0.2092 time to fit residues: 47.9665 Evaluate side-chains 141 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 85 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 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 152 ILE Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 180 MET 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 215 THR 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 22 GLN 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 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 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 69 LEU Chi-restraints excluded: chain sr residue 80 ASN 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: 30.0000 chunk 26 optimal weight: 50.0000 chunk 211 optimal weight: 20.0000 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: 30.0000 chunk 145 optimal weight: 20.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... se 47 GLN sf 34 HIS ** sh 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sm 10 GLN sm 78 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.046866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.042642 restraints weight = 314053.476| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.22 r_work: 0.3508 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 33217 Z= 0.518 Angle : 0.883 9.965 49476 Z= 0.493 Chirality : 0.057 0.384 6320 Planarity : 0.008 0.114 2647 Dihedral : 23.035 179.486 16032 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.36 % Favored : 91.47 % Rotamer: Outliers : 8.34 % Allowed : 25.50 % Favored : 66.16 % 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: -2.35 (0.23), residues: 1160 helix: -1.08 (0.30), residues: 247 sheet: -1.18 (0.34), residues: 235 loop : -1.93 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGsk 53 TYR 0.027 0.004 TYRsm 96 PHE 0.035 0.003 PHEsr 79 TRP 0.014 0.004 TRPsf 16 HIS 0.014 0.003 HISsb 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.52 (33217) covalent geometry : angle 0.88290 / 0.49 (49476) hydrogen bonds : bond 0.11461 / 8.08 ( 975) hydrogen bonds : angle 4.67552 / 3.87 ( 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 168 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 80 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: sC 16 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5582 (mp0) REVERT: sc 79 LYS cc_start: 0.7806 (tmtt) cc_final: 0.7528 (tmtt) REVERT: sc 207 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7368 (mmtp) REVERT: sf 104 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6528 (mtpp) REVERT: sh 195 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6649 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: sk 3 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6878 (mmt90) REVERT: sm 12 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.4968 (mt0) REVERT: sr 98 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6756 (p90) REVERT: sy 100 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8099 (pt) REVERT: sy 103 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6411 (t80) outliers start: 88 outliers final: 64 residues processed: 151 average time/residue: 0.2125 time to fit residues: 51.1611 Evaluate side-chains 150 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 76 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 sc residue 70 ILE Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 74 LEU 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 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 10 GLN Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 15 HIS 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 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 6 VAL 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 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 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: 0.8980 chunk 89 optimal weight: 30.0000 chunk 167 optimal weight: 7.9990 chunk 10 optimal weight: 60.0000 chunk 208 optimal weight: 0.0770 chunk 141 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 127 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 30 optimal weight: 50.0000 overall best weight: 3.9946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... se 47 GLN sm 10 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.048098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.043812 restraints weight = 311393.734| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.94 r_work: 0.3550 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4439 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= 0.140 Angle : 0.531 9.357 49476 Z= 0.320 Chirality : 0.037 0.292 6320 Planarity : 0.005 0.102 2647 Dihedral : 22.901 179.328 16032 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 6.16 % Allowed : 27.68 % Favored : 66.16 % 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: -0.44 (0.30), residues: 258 sheet: -0.76 (0.35), residues: 228 loop : -1.48 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsp 56 TYR 0.034 0.002 TYRsm 9 PHE 0.017 0.001 PHEsr 37 TRP 0.013 0.002 TRPse 31 HIS 0.004 0.001 HISsm 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (33217) covalent geometry : angle 0.53092 / 0.32 (49476) hydrogen bonds : bond 0.07596 / 5.32 ( 975) hydrogen bonds : angle 4.01415 / 3.27 ( 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 152 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 87 time to evaluate : 0.671 Fit side-chains REVERT: sc 79 LYS cc_start: 0.7797 (tmtt) cc_final: 0.7340 (tmtt) REVERT: se 79 GLU cc_start: 0.8397 (tp30) cc_final: 0.7439 (tp30) REVERT: se 86 TYR cc_start: 0.8900 (m-80) cc_final: 0.8594 (m-80) REVERT: sf 104 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6279 (mtpp) REVERT: sh 195 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6564 (mmm-85) REVERT: sj 22 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7548 (pp30) REVERT: sm 12 GLN cc_start: 0.5418 (OUTLIER) cc_final: 0.5144 (tt0) REVERT: sp 120 LYS cc_start: 0.7412 (tptt) cc_final: 0.7166 (tptp) REVERT: sr 36 GLU cc_start: 0.7520 (tt0) cc_final: 0.7319 (tm-30) REVERT: sr 57 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6986 (mtt90) REVERT: sr 98 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6001 (p90) REVERT: sy 74 LYS cc_start: 0.5766 (OUTLIER) cc_final: 0.5410 (pttt) REVERT: sy 100 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8186 (pt) REVERT: sy 103 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6144 (t80) outliers start: 65 outliers final: 44 residues processed: 134 average time/residue: 0.2044 time to fit residues: 44.0844 Evaluate side-chains 136 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 216 THR Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR 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 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU 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 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 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 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 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 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 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 74 LYS 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: 0.2980 chunk 163 optimal weight: 0.9980 chunk 55 optimal weight: 50.0000 chunk 87 optimal weight: 40.0000 chunk 92 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 209 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 6 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sm 10 GLN 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 = 0.3826 r_free = 0.3826 target = 0.048300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.043990 restraints weight = 312238.211| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.82 r_work: 0.3565 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33217 Z= 0.138 Angle : 0.500 9.379 49476 Z= 0.302 Chirality : 0.036 0.336 6320 Planarity : 0.005 0.104 2647 Dihedral : 22.710 178.635 16032 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 4.93 % Allowed : 28.82 % Favored : 66.26 % 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: -0.16 (0.31), residues: 258 sheet: -0.57 (0.36), residues: 214 loop : -1.31 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsr 78 TYR 0.029 0.002 TYRsm 9 PHE 0.019 0.001 PHEsr 79 TRP 0.009 0.002 TRPsy 20 HIS 0.004 0.001 HISsi 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (33217) covalent geometry : angle 0.50020 / 0.30 (49476) hydrogen bonds : bond 0.06930 / 4.82 ( 975) hydrogen bonds : angle 3.88184 / 3.18 ( 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 141 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 89 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sc 79 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7448 (tmtt) REVERT: se 79 GLU cc_start: 0.8376 (tp30) cc_final: 0.7392 (tp30) REVERT: se 86 TYR cc_start: 0.8824 (m-80) cc_final: 0.8586 (m-80) REVERT: sf 104 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6331 (mtpp) REVERT: sh 195 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5507 (tmm-80) REVERT: si 132 LEU cc_start: 0.7765 (pp) cc_final: 0.7179 (mt) REVERT: sj 22 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7577 (pp30) REVERT: sp 120 LYS cc_start: 0.7279 (tptt) cc_final: 0.7020 (tptp) REVERT: sr 98 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6124 (p90) REVERT: sy 74 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5395 (pttt) REVERT: sy 100 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8296 (pt) REVERT: sy 103 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6211 (t80) outliers start: 52 outliers final: 38 residues processed: 128 average time/residue: 0.1991 time to fit residues: 41.8802 Evaluate side-chains 131 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 86 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 THR Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR 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 204 GLU Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 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 14 THR Chi-restraints excluded: chain sk residue 17 VAL 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 39 MET 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 sr residue 45 GLN 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 74 LYS Chi-restraints excluded: chain sy residue 100 ILE 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: 10.0000 chunk 188 optimal weight: 20.0000 chunk 22 optimal weight: 40.0000 chunk 177 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 153 optimal weight: 0.0970 chunk 49 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sh 178 ASN ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sr 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.048227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.043904 restraints weight = 310740.991| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.94 r_work: 0.3553 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33217 Z= 0.163 Angle : 0.506 9.305 49476 Z= 0.303 Chirality : 0.036 0.361 6320 Planarity : 0.005 0.103 2647 Dihedral : 22.669 179.001 16030 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 4.93 % Allowed : 28.53 % Favored : 66.54 % 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: -1.28 (0.24), residues: 1160 helix: 0.02 (0.31), residues: 250 sheet: -0.58 (0.35), residues: 220 loop : -1.30 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGso 14 TYR 0.012 0.002 TYRsm 9 PHE 0.020 0.001 PHEsp 23 TRP 0.010 0.001 TRPsy 20 HIS 0.019 0.001 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (33217) covalent geometry : angle 0.50637 / 0.30 (49476) hydrogen bonds : bond 0.06970 / 4.85 ( 975) hydrogen bonds : angle 3.84601 / 3.15 ( 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 138 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 86 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sc 79 LYS cc_start: 0.7815 (tmtt) cc_final: 0.7415 (tmtt) REVERT: sc 212 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.8031 (t80) REVERT: se 79 GLU cc_start: 0.8365 (tp30) cc_final: 0.7371 (tp30) REVERT: se 86 TYR cc_start: 0.8850 (m-80) cc_final: 0.8599 (m-80) REVERT: sf 104 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6225 (mtpp) REVERT: sh 195 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.5401 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7625 (pp30) REVERT: sm 39 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6917 (ptp) REVERT: sp 120 LYS cc_start: 0.7336 (tptt) cc_final: 0.7066 (tptp) REVERT: sr 57 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7083 (mtt90) REVERT: sr 98 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.6131 (p90) REVERT: sy 74 LYS cc_start: 0.5632 (OUTLIER) cc_final: 0.5284 (pttt) REVERT: sy 100 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8075 (pt) REVERT: sy 103 PHE cc_start: 0.7277 (OUTLIER) cc_final: 0.6167 (t80) outliers start: 52 outliers final: 41 residues processed: 121 average time/residue: 0.1934 time to fit residues: 38.1090 Evaluate side-chains 136 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 155 THR 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 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sh residue 205 VAL 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 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR 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 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 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 80 ASN Chi-restraints excluded: chain sr residue 98 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 30.0000 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 70.0000 chunk 105 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 170 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 180 optimal weight: 6.9990 chunk 82 optimal weight: 40.0000 chunk 64 optimal weight: 50.0000 overall best weight: 15.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sm 16 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 = 0.3817 r_free = 0.3817 target = 0.048141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.043737 restraints weight = 309698.411| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.87 r_work: 0.3564 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 33217 Z= 0.265 Angle : 0.621 59.192 49476 Z= 0.375 Chirality : 0.040 0.472 6320 Planarity : 0.005 0.102 2647 Dihedral : 22.666 178.908 16030 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 5.21 % Allowed : 28.44 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % 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: -1.30 (0.24), residues: 1160 helix: -0.02 (0.31), residues: 250 sheet: -0.52 (0.36), residues: 214 loop : -1.32 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsy 3 TYR 0.013 0.002 TYRsi 131 PHE 0.013 0.002 PHEsp 23 TRP 0.011 0.002 TRPsy 20 HIS 0.018 0.001 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.27 (33217) covalent geometry : angle 0.62113 / 0.37 (49476) hydrogen bonds : bond 0.07049 / 4.91 ( 975) hydrogen bonds : angle 3.85834 / 3.16 ( 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 140 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 85 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: sc 79 LYS cc_start: 0.7815 (tmtt) cc_final: 0.7375 (tmtt) REVERT: sc 212 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.8032 (t80) REVERT: se 79 GLU cc_start: 0.8410 (tp30) cc_final: 0.7393 (tp30) REVERT: se 86 TYR cc_start: 0.8882 (m-80) cc_final: 0.8646 (m-80) REVERT: sf 104 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6211 (mtpp) REVERT: sh 195 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.5424 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7613 (pp30) REVERT: sp 120 LYS cc_start: 0.7313 (tptt) cc_final: 0.7060 (tptp) REVERT: sr 57 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7068 (mtt90) REVERT: sr 98 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6051 (p90) REVERT: sy 74 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.5171 (pttt) REVERT: sy 100 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8034 (pt) REVERT: sy 103 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6169 (t80) outliers start: 55 outliers final: 44 residues processed: 122 average time/residue: 0.2053 time to fit residues: 40.9508 Evaluate side-chains 137 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 84 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 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 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 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain sh residue 203 ILE Chi-restraints excluded: chain sh residue 205 VAL 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 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR 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 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 111 LEU 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 sr residue 115 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 4.9990 chunk 179 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 19 optimal weight: 50.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3817 r_free = 0.3817 target = 0.048141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.043734 restraints weight = 312222.897| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.87 r_work: 0.3563 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 33217 Z= 0.265 Angle : 0.621 59.192 49476 Z= 0.375 Chirality : 0.040 0.472 6320 Planarity : 0.005 0.102 2647 Dihedral : 22.666 178.908 16030 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 5.02 % Allowed : 28.53 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.09 % 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: -1.30 (0.24), residues: 1160 helix: -0.02 (0.31), residues: 250 sheet: -0.52 (0.36), residues: 214 loop : -1.32 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsy 3 TYR 0.013 0.002 TYRsi 131 PHE 0.013 0.002 PHEsp 23 TRP 0.011 0.002 TRPsy 20 HIS 0.018 0.001 HISsp 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.27 (33217) covalent geometry : angle 0.62113 / 0.37 (49476) hydrogen bonds : bond 0.07049 / 4.91 ( 975) hydrogen bonds : angle 3.85834 / 3.16 ( 1892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6345.50 seconds wall clock time: 110 minutes 26.28 seconds (6626.28 seconds total)