Starting phenix.real_space_refine on Sat Feb 7 05:55:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.map" model { file = "/net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v29_64721/02_2026/9v29_64721.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 966 5.49 5 S 59 5.16 5 C 15478 2.51 5 N 5677 2.21 5 O 8420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 6.39, per 1000 atoms: 0.21 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: 5.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.11 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: 9.78 Time building geometry restraints manager: 3.61 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=" C5' Csa1090 " pdb=" C4' Csa1090 " ideal model delta sigma weight residual 1.508 1.470 0.038 1.50e-02 4.44e+03 6.51e+00 ... (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=" C4' Csa1090 " pdb=" C3' Csa1090 " pdb=" O3' Csa1090 " ideal model delta sigma weight residual 113.00 122.07 -9.07 1.50e+00 4.44e-01 3.65e+01 angle pdb=" C4' Asa 295 " pdb=" C3' Asa 295 " pdb=" O3' Asa 295 " ideal model delta sigma weight residual 113.00 120.17 -7.17 1.50e+00 4.44e-01 2.28e+01 angle pdb=" CA GLNsr 45 " pdb=" CB GLNsr 45 " pdb=" CG GLNsr 45 " ideal model delta sigma weight residual 114.10 123.63 -9.53 2.00e+00 2.50e-01 2.27e+01 angle pdb=" O4' Asa 295 " pdb=" C4' Asa 295 " pdb=" C3' Asa 295 " ideal model delta sigma weight residual 104.00 99.46 4.54 1.00e+00 1.00e+00 2.06e+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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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= 0.214 Angle : 0.620 20.451 49476 Z= 0.324 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 covalent geometry : bond 0.00400 (33217) covalent geometry : angle 0.61995 (49476) hydrogen bonds : bond 0.17117 ( 975) hydrogen bonds : angle 6.42860 ( 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 : 0.671 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: 0.2035 time to fit residues: 41.9252 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 : 0.556 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sc 133 GLN sc 227 GLN se 62 GLN sf 31 HIS ** sh 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sm 16 HIS sm 116 GLN sp 27 HIS sr 45 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.048056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.043601 restraints weight = 315168.106| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.90 r_work: 0.3552 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 33217 Z= 0.299 Angle : 0.728 13.145 49476 Z= 0.369 Chirality : 0.040 0.274 6320 Planarity : 0.006 0.104 2647 Dihedral : 22.950 179.692 16052 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.64 % Favored : 93.10 % Rotamer: Outliers : 7.39 % Allowed : 24.83 % Favored : 67.77 % 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: -1.74 (0.24), residues: 1160 helix: -0.64 (0.30), residues: 258 sheet: -0.93 (0.33), residues: 237 loop : -1.44 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGsh 195 TYR 0.016 0.002 TYRsc 145 PHE 0.014 0.002 PHEsr 86 TRP 0.014 0.003 TRPse 31 HIS 0.009 0.002 HISsm 16 Details of bonding type rmsd covalent geometry : bond 0.00580 (33217) covalent geometry : angle 0.72828 (49476) hydrogen bonds : bond 0.07673 ( 975) hydrogen bonds : angle 4.23382 ( 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 169 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 91 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6519 (tpt170) REVERT: sC 16 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5448 (mp0) REVERT: sc 81 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: sc 83 MET cc_start: 0.8616 (mmt) cc_final: 0.8296 (mmt) REVERT: sc 131 MET cc_start: 0.9075 (mtt) cc_final: 0.8871 (mtt) REVERT: se 86 TYR cc_start: 0.8960 (m-80) cc_final: 0.8674 (m-80) REVERT: sf 15 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7730 (p-80) REVERT: sf 180 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7228 (tpt) REVERT: sh 195 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6613 (mmm-85) REVERT: sm 12 GLN cc_start: 0.5303 (OUTLIER) cc_final: 0.4995 (tt0) REVERT: sp 23 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7709 (t80) REVERT: sp 120 LYS cc_start: 0.7161 (tmtt) cc_final: 0.6616 (tptp) REVERT: sr 36 GLU cc_start: 0.6997 (tt0) cc_final: 0.6696 (tt0) REVERT: sr 41 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8401 (ttp) REVERT: sr 57 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7070 (mtt90) REVERT: sr 98 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6658 (p90) REVERT: sr 115 GLU cc_start: 0.8601 (pm20) cc_final: 0.8296 (pm20) REVERT: sy 100 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8088 (pt) REVERT: sy 103 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6090 (t80) REVERT: sy 106 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6558 (mtm-85) outliers start: 78 outliers final: 37 residues processed: 152 average time/residue: 0.2136 time to fit residues: 51.6701 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 : 0.614 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 81 GLU Chi-restraints excluded: chain sc residue 197 ASP Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 62 GLN Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 103 THR 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 sh residue 186 ASN 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 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 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 so residue 96 VAL Chi-restraints excluded: chain sp residue 23 PHE Chi-restraints excluded: chain sp residue 25 VAL Chi-restraints excluded: chain sp residue 49 ILE Chi-restraints excluded: chain sp residue 67 TYR Chi-restraints excluded: chain sp residue 76 VAL Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sr residue 41 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 54 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sB 20 ASN sc 133 GLN se 47 GLN ** sh 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** sr 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.048021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.043631 restraints weight = 314378.008| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.83 r_work: 0.3555 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33217 Z= 0.248 Angle : 0.645 9.086 49476 Z= 0.330 Chirality : 0.038 0.273 6320 Planarity : 0.005 0.101 2647 Dihedral : 22.787 178.961 16039 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 6.45 % Allowed : 25.59 % Favored : 67.96 % 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: -1.48 (0.24), residues: 1160 helix: -0.22 (0.31), residues: 248 sheet: -0.81 (0.34), residues: 232 loop : -1.34 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsr 28 TYR 0.012 0.002 TYRsm 96 PHE 0.012 0.002 PHEse 26 TRP 0.015 0.002 TRPse 31 HIS 0.006 0.001 HISsr 44 Details of bonding type rmsd covalent geometry : bond 0.00478 (33217) covalent geometry : angle 0.64523 (49476) hydrogen bonds : bond 0.06956 ( 975) hydrogen bonds : angle 4.03994 ( 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 158 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 90 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6588 (tpt170) REVERT: se 86 TYR cc_start: 0.8992 (m-80) cc_final: 0.8694 (m-80) REVERT: sf 15 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7693 (p-80) REVERT: sf 180 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7023 (tpt) REVERT: sf 195 LYS cc_start: 0.8116 (pttm) cc_final: 0.7882 (pttm) REVERT: sh 195 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.5260 (tmm-80) REVERT: sm 12 GLN cc_start: 0.5186 (OUTLIER) cc_final: 0.4613 (mt0) REVERT: sp 23 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7737 (t80) REVERT: sr 98 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6216 (p90) REVERT: sr 112 ASP cc_start: 0.7548 (p0) cc_final: 0.7301 (p0) REVERT: sy 100 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7992 (pt) REVERT: sy 103 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6087 (t80) outliers start: 68 outliers final: 39 residues processed: 142 average time/residue: 0.2018 time to fit residues: 46.2130 Evaluate side-chains 134 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 74 LEU Chi-restraints excluded: chain sc residue 197 ASP 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 sf residue 15 HIS Chi-restraints excluded: chain sf residue 103 THR 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 sh residue 186 ASN Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 95 THR 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 51 THR Chi-restraints excluded: chain sm residue 59 PHE 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 sp residue 23 PHE 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 69 LEU Chi-restraints excluded: chain sr residue 80 ASN Chi-restraints excluded: chain sr residue 98 HIS Chi-restraints excluded: chain sy residue 32 THR Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 100 ILE Chi-restraints excluded: chain sy residue 103 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 145 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 165 optimal weight: 0.0470 overall best weight: 9.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sc 211 ASN sc 222 GLN sm 138 ASN sr 44 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.047724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.043350 restraints weight = 313396.002| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.76 r_work: 0.3543 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33217 Z= 0.280 Angle : 0.682 9.230 49476 Z= 0.348 Chirality : 0.039 0.348 6320 Planarity : 0.005 0.103 2647 Dihedral : 22.767 179.293 16034 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 6.92 % Allowed : 26.73 % Favored : 66.35 % 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: -1.58 (0.24), residues: 1160 helix: -0.40 (0.30), residues: 254 sheet: -0.82 (0.35), residues: 226 loop : -1.38 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsk 53 TYR 0.014 0.002 TYRsm 96 PHE 0.013 0.002 PHEsp 23 TRP 0.010 0.002 TRPse 31 HIS 0.006 0.001 HISsr 44 Details of bonding type rmsd covalent geometry : bond 0.00539 (33217) covalent geometry : angle 0.68177 (49476) hydrogen bonds : bond 0.07253 ( 975) hydrogen bonds : angle 3.97458 ( 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 160 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 87 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6570 (tpt170) REVERT: sc 79 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7186 (tmtt) REVERT: sc 212 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7883 (t80) REVERT: sf 15 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7774 (p-80) REVERT: sf 104 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6460 (mtpp) REVERT: sf 180 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7058 (tpt) REVERT: sj 22 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: sm 12 GLN cc_start: 0.5303 (OUTLIER) cc_final: 0.4917 (tt0) REVERT: sp 120 LYS cc_start: 0.7156 (tmtt) cc_final: 0.6879 (tptp) REVERT: sr 41 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8129 (ttp) REVERT: sr 57 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7031 (mtt90) REVERT: sr 98 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.5850 (p90) REVERT: sy 100 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7999 (pt) REVERT: sy 103 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6165 (t80) outliers start: 73 outliers final: 50 residues processed: 143 average time/residue: 0.1996 time to fit residues: 45.5665 Evaluate side-chains 145 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 83 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 85 ARG 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 212 PHE Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 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 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 186 ASN Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sk residue 10 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 15 HIS Chi-restraints excluded: chain sm residue 39 MET Chi-restraints excluded: chain sm residue 51 THR 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 sm residue 147 THR 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 sp residue 135 THR Chi-restraints excluded: chain sr residue 41 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 24 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.047776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.043413 restraints weight = 314094.344| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.76 r_work: 0.3546 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33217 Z= 0.266 Angle : 0.657 9.189 49476 Z= 0.336 Chirality : 0.039 0.411 6320 Planarity : 0.005 0.103 2647 Dihedral : 22.733 178.303 16032 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 7.20 % Allowed : 26.54 % 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: -1.51 (0.24), residues: 1160 helix: -0.27 (0.30), residues: 257 sheet: -0.72 (0.35), residues: 230 loop : -1.41 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsp 123 TYR 0.013 0.002 TYRsm 96 PHE 0.031 0.002 PHEsp 23 TRP 0.011 0.002 TRPsy 20 HIS 0.005 0.001 HISsb 138 Details of bonding type rmsd covalent geometry : bond 0.00512 (33217) covalent geometry : angle 0.65670 (49476) hydrogen bonds : bond 0.06829 ( 975) hydrogen bonds : angle 3.89008 ( 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 163 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 87 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6596 (tpt170) REVERT: sC 16 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.5019 (mp0) REVERT: sc 79 LYS cc_start: 0.7653 (tmtt) cc_final: 0.7306 (tmtt) REVERT: sc 212 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7930 (t80) REVERT: se 79 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: sf 15 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7780 (p-80) REVERT: sf 104 LYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6356 (mtpp) REVERT: sf 180 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7153 (tpt) REVERT: sh 195 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.5972 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: sj 59 ARG cc_start: 0.5057 (ptt-90) cc_final: 0.4526 (ptt-90) REVERT: sm 12 GLN cc_start: 0.5227 (OUTLIER) cc_final: 0.4938 (tt0) REVERT: sr 57 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7014 (mtt90) REVERT: sr 98 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.5924 (p90) REVERT: sy 100 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8037 (pt) REVERT: sy 103 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6256 (t80) outliers start: 76 outliers final: 51 residues processed: 144 average time/residue: 0.1965 time to fit residues: 45.9657 Evaluate side-chains 148 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 83 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 212 PHE Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 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 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 186 ASN Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL 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 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 51 THR 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 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: 5.9990 chunk 105 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 chunk 211 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 overall best weight: 10.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.047616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.043318 restraints weight = 313822.585| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.85 r_work: 0.3532 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 33217 Z= 0.292 Angle : 0.689 9.355 49476 Z= 0.351 Chirality : 0.040 0.458 6320 Planarity : 0.005 0.104 2647 Dihedral : 22.758 179.084 16029 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 7.20 % Allowed : 27.49 % Favored : 65.31 % 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: -1.59 (0.24), residues: 1160 helix: -0.28 (0.30), residues: 257 sheet: -0.78 (0.35), residues: 229 loop : -1.48 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsk 53 TYR 0.015 0.002 TYRsm 96 PHE 0.009 0.002 PHEsp 23 TRP 0.011 0.002 TRPsy 20 HIS 0.011 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00563 (33217) covalent geometry : angle 0.68898 (49476) hydrogen bonds : bond 0.07227 ( 975) hydrogen bonds : angle 3.95837 ( 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 159 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 83 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.6541 (tpt170) REVERT: sC 16 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.5119 (mp0) REVERT: sc 207 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7288 (mmtp) REVERT: se 79 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: sf 15 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7863 (p-80) REVERT: sf 104 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6303 (mtpp) REVERT: sf 180 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7264 (tpt) REVERT: sh 160 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7809 (mmp) REVERT: sh 195 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.5324 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: sj 59 ARG cc_start: 0.5133 (ptt-90) cc_final: 0.4617 (ptt-90) REVERT: sj 62 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7821 (p0) REVERT: sm 12 GLN cc_start: 0.5324 (OUTLIER) cc_final: 0.4956 (tt0) REVERT: sr 57 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7175 (mtt90) REVERT: sr 98 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6047 (p90) REVERT: sy 100 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8275 (pt) REVERT: sy 103 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6259 (t80) outliers start: 76 outliers final: 56 residues processed: 144 average time/residue: 0.1848 time to fit residues: 43.7521 Evaluate side-chains 153 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 81 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 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 204 GLU Chi-restraints excluded: chain sf residue 215 THR Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 160 MET Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 186 ASN Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 62 ASN Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 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 sm residue 125 ILE Chi-restraints excluded: chain sm residue 147 THR 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 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 44 HIS 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 sr residue 115 GLU 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: 9.9990 chunk 89 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 208 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 overall best weight: 9.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: si 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.047564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.043274 restraints weight = 309642.256| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.74 r_work: 0.3553 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33217 Z= 0.263 Angle : 0.659 9.173 49476 Z= 0.337 Chirality : 0.039 0.449 6320 Planarity : 0.005 0.103 2647 Dihedral : 22.724 178.568 16029 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 7.01 % Allowed : 28.15 % Favored : 64.83 % 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: -1.57 (0.24), residues: 1160 helix: -0.25 (0.31), residues: 257 sheet: -0.83 (0.35), residues: 231 loop : -1.45 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsk 53 TYR 0.013 0.002 TYRsm 96 PHE 0.017 0.002 PHEsp 23 TRP 0.022 0.002 TRPsj 67 HIS 0.013 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00508 (33217) covalent geometry : angle 0.65897 (49476) hydrogen bonds : bond 0.06722 ( 975) hydrogen bonds : angle 3.89645 ( 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 158 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 84 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6568 (tpt-90) REVERT: sC 16 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5104 (mp0) REVERT: sc 207 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7326 (mmtp) REVERT: se 79 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: sf 15 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7843 (p-80) REVERT: sf 104 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6361 (mtpp) REVERT: sf 180 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7077 (tpt) REVERT: sj 22 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7660 (pp30) REVERT: sj 59 ARG cc_start: 0.4963 (ptt-90) cc_final: 0.4457 (ptt-90) REVERT: sj 62 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7822 (p0) REVERT: sm 12 GLN cc_start: 0.5147 (OUTLIER) cc_final: 0.4857 (tt0) REVERT: sp 23 PHE cc_start: 0.7527 (t80) cc_final: 0.7301 (t80) REVERT: sr 57 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7037 (mtt90) REVERT: sr 98 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.6207 (p90) REVERT: sy 74 LYS cc_start: 0.5472 (OUTLIER) cc_final: 0.5037 (pttt) REVERT: sy 103 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6226 (t80) outliers start: 74 outliers final: 53 residues processed: 140 average time/residue: 0.1991 time to fit residues: 44.9444 Evaluate side-chains 148 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 81 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 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 204 GLU Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 186 ASN Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 29 MET Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 62 ASN Chi-restraints excluded: chain sk residue 10 ILE Chi-restraints excluded: chain sk residue 14 THR Chi-restraints excluded: chain sk residue 17 VAL Chi-restraints excluded: chain sk residue 54 THR Chi-restraints excluded: chain sm residue 11 LYS Chi-restraints excluded: chain sm residue 12 GLN Chi-restraints excluded: chain sm residue 13 VAL Chi-restraints excluded: chain sm residue 51 THR 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 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 44 HIS 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 sr residue 115 GLU Chi-restraints excluded: chain sy residue 31 VAL Chi-restraints excluded: chain sy residue 39 LEU Chi-restraints excluded: chain sy residue 74 LYS 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: 9.9990 chunk 163 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 209 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 143 optimal weight: 30.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sf 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.047521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.043280 restraints weight = 312130.423| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.96 r_work: 0.3529 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33217 Z= 0.310 Angle : 0.710 9.367 49476 Z= 0.361 Chirality : 0.041 0.419 6320 Planarity : 0.005 0.105 2647 Dihedral : 22.794 179.168 16029 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 7.87 % Allowed : 27.87 % Favored : 64.27 % 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: -1.70 (0.24), residues: 1160 helix: -0.43 (0.30), residues: 257 sheet: -0.94 (0.35), residues: 231 loop : -1.50 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsk 53 TYR 0.043 0.002 TYRsi 131 PHE 0.020 0.002 PHEsp 23 TRP 0.022 0.003 TRPsj 67 HIS 0.008 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00598 (33217) covalent geometry : angle 0.71050 (49476) hydrogen bonds : bond 0.07303 ( 975) hydrogen bonds : angle 4.00149 ( 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 163 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 80 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.6447 (tpt170) REVERT: sC 16 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5279 (mp0) REVERT: sc 207 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7324 (mmtp) REVERT: se 79 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: sf 15 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7936 (p-80) REVERT: sf 104 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6420 (mtpp) REVERT: sf 180 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7414 (tpt) REVERT: sh 195 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6427 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: sj 59 ARG cc_start: 0.4997 (ptt-90) cc_final: 0.4474 (ptt-90) REVERT: sj 62 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7843 (p0) REVERT: sm 10 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6393 (mm-40) REVERT: sm 12 GLN cc_start: 0.5289 (OUTLIER) cc_final: 0.4914 (tt0) REVERT: sr 57 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7291 (mtt90) REVERT: sr 98 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6248 (p90) REVERT: sy 74 LYS cc_start: 0.5593 (OUTLIER) cc_final: 0.5119 (pttt) REVERT: sy 100 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8228 (pt) REVERT: sy 103 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6233 (t80) outliers start: 83 outliers final: 58 residues processed: 146 average time/residue: 0.2029 time to fit residues: 47.5758 Evaluate side-chains 154 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 79 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 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 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 15 HIS Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 103 THR Chi-restraints excluded: chain sf residue 104 LYS Chi-restraints excluded: chain sf residue 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 204 GLU Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 186 ASN Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 29 MET Chi-restraints excluded: chain sj residue 53 ILE Chi-restraints excluded: chain sj residue 62 ASN 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 13 VAL 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 sm residue 125 ILE Chi-restraints excluded: chain sm residue 147 THR 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 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 44 HIS 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 sr residue 115 GLU Chi-restraints excluded: chain sy residue 31 VAL 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: 20.0000 chunk 188 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.047634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.043312 restraints weight = 310347.177| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.74 r_work: 0.3545 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 33217 Z= 0.294 Angle : 0.691 9.130 49476 Z= 0.351 Chirality : 0.040 0.431 6320 Planarity : 0.005 0.104 2647 Dihedral : 22.781 178.594 16029 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 7.58 % Allowed : 27.77 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.24), residues: 1160 helix: -0.41 (0.31), residues: 257 sheet: -0.79 (0.36), residues: 224 loop : -1.51 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsk 53 TYR 0.041 0.002 TYRsi 131 PHE 0.014 0.002 PHEsp 23 TRP 0.023 0.003 TRPsj 67 HIS 0.008 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00568 (33217) covalent geometry : angle 0.69138 (49476) hydrogen bonds : bond 0.06873 ( 975) hydrogen bonds : angle 3.95807 ( 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 160 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 80 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.6589 (tpt-90) REVERT: sC 16 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5257 (mp0) REVERT: sc 207 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7300 (mmtp) REVERT: se 79 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7750 (tp30) REVERT: sf 40 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8338 (tp) REVERT: sf 104 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6429 (mtpp) REVERT: sf 180 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7137 (tpt) REVERT: sh 195 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6092 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: sj 59 ARG cc_start: 0.4923 (ptt-90) cc_final: 0.4376 (ptt-90) REVERT: sj 62 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7797 (p0) REVERT: sj 216 GLU cc_start: 0.8034 (mp0) cc_final: 0.7719 (mp0) REVERT: sm 10 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6323 (mm-40) REVERT: sm 12 GLN cc_start: 0.5209 (OUTLIER) cc_final: 0.4828 (tt0) REVERT: sr 57 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7196 (mtt90) REVERT: sr 98 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6394 (p90) REVERT: sy 74 LYS cc_start: 0.5787 (OUTLIER) cc_final: 0.5574 (pttt) REVERT: sy 100 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8318 (pt) REVERT: sy 103 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6236 (t80) outliers start: 80 outliers final: 57 residues processed: 141 average time/residue: 0.2099 time to fit residues: 47.7174 Evaluate side-chains 154 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 80 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sC residue 16 GLU Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET 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 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain se residue 155 THR Chi-restraints excluded: chain sf residue 19 SER Chi-restraints excluded: chain sf residue 40 LEU 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 204 GLU Chi-restraints excluded: chain sf residue 220 LEU Chi-restraints excluded: chain sh residue 170 VAL Chi-restraints excluded: chain sh residue 186 ASN Chi-restraints excluded: chain sh residue 195 ARG Chi-restraints excluded: chain sh residue 198 ILE Chi-restraints excluded: chain si residue 127 VAL Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 29 MET Chi-restraints excluded: chain sj residue 62 ASN 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 5 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 13 VAL 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 sm residue 125 ILE Chi-restraints excluded: chain sm residue 147 THR 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 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 44 HIS 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 sr residue 115 GLU Chi-restraints excluded: chain sy residue 31 VAL 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: 6.9990 chunk 136 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.047879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.043571 restraints weight = 307687.765| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.66 r_work: 0.3557 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33217 Z= 0.227 Angle : 0.633 11.229 49476 Z= 0.324 Chirality : 0.037 0.402 6320 Planarity : 0.005 0.102 2647 Dihedral : 22.704 178.403 16029 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 6.64 % Allowed : 28.34 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.24), residues: 1160 helix: -0.23 (0.31), residues: 258 sheet: -0.78 (0.35), residues: 226 loop : -1.46 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsk 53 TYR 0.039 0.002 TYRsi 131 PHE 0.010 0.001 PHEsp 23 TRP 0.020 0.002 TRPsj 67 HIS 0.006 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00437 (33217) covalent geometry : angle 0.63331 (49476) hydrogen bonds : bond 0.06285 ( 975) hydrogen bonds : angle 3.82418 ( 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 154 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 84 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: sB 85 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6560 (tpt-90) REVERT: sc 207 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7275 (mmtp) REVERT: se 79 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: sf 40 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8367 (tp) REVERT: sf 104 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6485 (mtpp) REVERT: sf 180 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7494 (tpt) REVERT: sh 160 MET cc_start: 0.7509 (mmp) cc_final: 0.6370 (ttp) REVERT: sh 195 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6205 (tmm-80) REVERT: sj 22 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7621 (pp30) REVERT: sj 59 ARG cc_start: 0.4840 (ptt-90) cc_final: 0.4298 (ptt-90) REVERT: sj 62 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7838 (p0) REVERT: sj 216 GLU cc_start: 0.8053 (mp0) cc_final: 0.7727 (mp0) REVERT: sm 10 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6292 (mm-40) REVERT: sm 12 GLN cc_start: 0.5025 (OUTLIER) cc_final: 0.4713 (tt0) REVERT: sr 57 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7196 (mtt90) REVERT: sy 100 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8309 (pt) REVERT: sy 103 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6162 (t80) outliers start: 70 outliers final: 51 residues processed: 135 average time/residue: 0.2179 time to fit residues: 46.9869 Evaluate side-chains 145 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 80 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 85 ARG Chi-restraints excluded: chain sB residue 90 THR Chi-restraints excluded: chain sb residue 144 SER Chi-restraints excluded: chain sc residue 71 VAL Chi-restraints excluded: chain sc residue 83 MET Chi-restraints excluded: chain sc residue 172 VAL Chi-restraints excluded: chain sc residue 207 LYS Chi-restraints excluded: chain sc residue 216 THR Chi-restraints excluded: chain sc residue 220 VAL Chi-restraints excluded: chain se residue 49 VAL Chi-restraints excluded: chain se residue 79 GLU Chi-restraints excluded: chain se residue 105 LEU Chi-restraints excluded: chain se residue 125 THR Chi-restraints excluded: chain se residue 152 ILE Chi-restraints excluded: chain 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 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 204 GLU 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 127 VAL Chi-restraints excluded: chain sj residue 3 ILE Chi-restraints excluded: chain sj residue 7 SER Chi-restraints excluded: chain sj residue 22 GLN Chi-restraints excluded: chain sj residue 29 MET Chi-restraints excluded: chain sj residue 62 ASN 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 12 GLN 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 sm residue 147 THR 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 67 TYR Chi-restraints excluded: chain sp residue 82 ASP Chi-restraints excluded: chain sp residue 98 VAL Chi-restraints excluded: chain sp residue 111 LEU Chi-restraints excluded: chain sp residue 135 THR Chi-restraints excluded: chain sr residue 44 HIS 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 115 GLU Chi-restraints excluded: chain sy residue 31 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 148 optimal weight: 40.0000 chunk 140 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.047614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.043274 restraints weight = 310689.588| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.75 r_work: 0.3542 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33217 Z= 0.281 Angle : 0.686 10.515 49476 Z= 0.348 Chirality : 0.039 0.408 6320 Planarity : 0.005 0.104 2647 Dihedral : 22.758 178.718 16027 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 6.35 % Allowed : 28.72 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.24), residues: 1160 helix: -0.34 (0.31), residues: 258 sheet: -0.84 (0.35), residues: 227 loop : -1.49 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGso 127 TYR 0.039 0.002 TYRsi 131 PHE 0.011 0.002 PHEsp 23 TRP 0.019 0.002 TRPsj 67 HIS 0.006 0.001 HISsp 89 Details of bonding type rmsd covalent geometry : bond 0.00544 (33217) covalent geometry : angle 0.68589 (49476) hydrogen bonds : bond 0.06866 ( 975) hydrogen bonds : angle 3.91418 ( 1892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.70 seconds wall clock time: 113 minutes 19.04 seconds (6799.04 seconds total)