Starting phenix.real_space_refine on Fri Aug 7 16:15:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.map" model { file = "/net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v1k_64696/08_2026/9v1k_64696.cif" } resolution = 3.4 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 475 5.49 5 S 80 5.16 5 C 12351 2.51 5 N 4091 2.21 5 O 5459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22456 Number of models: 1 Model: "" Number of chains: 14 Chain: "sA" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 554 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "sD" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "sE" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 442 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "sG" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1395 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 2, 'TRANS': 178} Chain breaks: 10 Chain: "sa" Number of atoms: 10153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 10153 Classifications: {'RNA': 475} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 35, 'rna3p_pur': 225, 'rna3p_pyr': 171} Link IDs: {'rna2p': 79, 'rna3p': 395} Chain breaks: 2 Chain: "sd" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "sg" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1463 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain breaks: 1 Chain: "sl" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 2 Chain: "sq" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 842 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain breaks: 1 Chain: "ss" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1104 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "st" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 629 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "su" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1163 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "sv" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1245 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "sw" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 763 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Time building chain proxies: 4.73, per 1000 atoms: 0.21 Number of scatterers: 22456 At special positions: 0 Unit cell: (110.21, 135.89, 147.66, 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 80 16.00 P 475 15.00 O 5459 8.00 N 4091 7.00 C 12351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSsE 24 " - pdb=" SG CYSsE 42 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 740.0 milliseconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 40.5% alpha, 14.0% beta 127 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'sA' and resid 51 through 62 removed outlier: 3.696A pdb=" N GLUsA 61 " --> pdb=" O LYSsA 57 " (cutoff:3.500A) Processing helix chain 'sA' and resid 63 through 65 No H-bonds generated for 'chain 'sA' and resid 63 through 65' Processing helix chain 'sA' and resid 69 through 77 removed outlier: 4.134A pdb=" N ASPsA 75 " --> pdb=" O ALAsA 71 " (cutoff:3.500A) Processing helix chain 'sA' and resid 80 through 94 removed outlier: 3.690A pdb=" N ILEsA 86 " --> pdb=" O SERsA 82 " (cutoff:3.500A) Processing helix chain 'sE' and resid 32 through 36 Processing helix chain 'sE' and resid 46 through 51 Processing helix chain 'sd' and resid 20 through 41 removed outlier: 3.585A pdb=" N PHEsd 25 " --> pdb=" O ARGsd 21 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VALsd 26 " --> pdb=" O LYSsd 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLUsd 37 " --> pdb=" O ALAsd 33 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARGsd 41 " --> pdb=" O GLUsd 37 " (cutoff:3.500A) Processing helix chain 'sd' and resid 78 through 92 Processing helix chain 'sd' and resid 94 through 96 No H-bonds generated for 'chain 'sd' and resid 94 through 96' Processing helix chain 'sd' and resid 107 through 110 Processing helix chain 'sd' and resid 111 through 126 removed outlier: 3.649A pdb=" N GLUsd 117 " --> pdb=" O VALsd 113 " (cutoff:3.500A) Processing helix chain 'sd' and resid 128 through 143 removed outlier: 3.668A pdb=" N ASPsd 142 " --> pdb=" O ARGsd 138 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SERsd 143 " --> pdb=" O LEUsd 139 " (cutoff:3.500A) Processing helix chain 'sd' and resid 176 through 181 removed outlier: 3.860A pdb=" N GLNsd 180 " --> pdb=" O ASNsd 176 " (cutoff:3.500A) Processing helix chain 'sg' and resid 64 through 68 Processing helix chain 'sg' and resid 69 through 78 Processing helix chain 'sg' and resid 87 through 107 Processing helix chain 'sg' and resid 109 through 122 removed outlier: 3.589A pdb=" N ASPsg 116 " --> pdb=" O GLNsg 112 " (cutoff:3.500A) Processing helix chain 'sg' and resid 144 through 165 Processing helix chain 'sg' and resid 170 through 184 removed outlier: 3.501A pdb=" N ASNsg 181 " --> pdb=" O ASPsg 177 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYSsg 184 " --> pdb=" O VALsg 180 " (cutoff:3.500A) Processing helix chain 'sg' and resid 189 through 204 Processing helix chain 'sl' and resid 4 through 13 removed outlier: 3.630A pdb=" N ILEsl 9 " --> pdb=" O THRsl 5 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALAsl 10 " --> pdb=" O LYSsl 6 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILEsl 11 " --> pdb=" O ASPsl 7 " (cutoff:3.500A) Processing helix chain 'sl' and resid 37 through 50 removed outlier: 3.654A pdb=" N VALsl 41 " --> pdb=" O PROsl 37 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THRsl 50 " --> pdb=" O LYSsl 46 " (cutoff:3.500A) Processing helix chain 'sl' and resid 71 through 78 Processing helix chain 'sq' and resid 20 through 26 Processing helix chain 'sq' and resid 28 through 34 removed outlier: 3.925A pdb=" N LYSsq 34 " --> pdb=" O ALAsq 30 " (cutoff:3.500A) Processing helix chain 'sq' and resid 37 through 46 Processing helix chain 'sq' and resid 49 through 65 removed outlier: 4.058A pdb=" N LEUsq 55 " --> pdb=" O LYSsq 51 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYSsq 63 " --> pdb=" O LEUsq 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYSsq 64 " --> pdb=" O LEUsq 60 " (cutoff:3.500A) Processing helix chain 'sq' and resid 85 through 89 Processing helix chain 'sq' and resid 107 through 111 removed outlier: 3.696A pdb=" N LEUsq 111 " --> pdb=" O PROsq 108 " (cutoff:3.500A) Processing helix chain 'sq' and resid 114 through 119 removed outlier: 3.506A pdb=" N GLUsq 117 " --> pdb=" O TYRsq 114 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHEsq 118 " --> pdb=" O LEUsq 115 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SERsq 119 " --> pdb=" O GLYsq 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'sq' and resid 114 through 119' Processing helix chain 'ss' and resid 56 through 58 No H-bonds generated for 'chain 'ss' and resid 56 through 58' Processing helix chain 'ss' and resid 59 through 64 Processing helix chain 'ss' and resid 64 through 70 removed outlier: 3.922A pdb=" N VALss 70 " --> pdb=" O PROss 66 " (cutoff:3.500A) Processing helix chain 'ss' and resid 71 through 76 removed outlier: 3.544A pdb=" N ASNss 74 " --> pdb=" O GLYss 71 " (cutoff:3.500A) Processing helix chain 'ss' and resid 91 through 111 removed outlier: 4.386A pdb=" N ARGss 97 " --> pdb=" O ALAss 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLNss 98 " --> pdb=" O TYRss 94 " (cutoff:3.500A) Processing helix chain 'ss' and resid 113 through 128 Processing helix chain 'ss' and resid 129 through 132 Processing helix chain 'st' and resid 6 through 20 removed outlier: 3.699A pdb=" N ALAst 12 " --> pdb=" O THRst 8 " (cutoff:3.500A) Processing helix chain 'st' and resid 27 through 39 removed outlier: 3.886A pdb=" N ARGst 33 " --> pdb=" O HISst 29 " (cutoff:3.500A) Processing helix chain 'st' and resid 43 through 64 removed outlier: 3.592A pdb=" N THRst 55 " --> pdb=" O ALAst 51 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HISst 56 " --> pdb=" O GLYst 52 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYSst 63 " --> pdb=" O ARGst 59 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLYst 64 " --> pdb=" O ARGst 60 " (cutoff:3.500A) Processing helix chain 'st' and resid 71 through 77 Processing helix chain 'su' and resid 26 through 31 Processing helix chain 'su' and resid 32 through 34 No H-bonds generated for 'chain 'su' and resid 32 through 34' Processing helix chain 'su' and resid 39 through 50 Processing helix chain 'su' and resid 56 through 60 Processing helix chain 'su' and resid 61 through 74 removed outlier: 3.608A pdb=" N ILEsu 65 " --> pdb=" O THRsu 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLUsu 66 " --> pdb=" O PROsu 62 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYSsu 67 " --> pdb=" O ALAsu 63 " (cutoff:3.500A) Processing helix chain 'su' and resid 75 through 79 removed outlier: 3.739A pdb=" N LYSsu 79 " --> pdb=" O LEUsu 76 " (cutoff:3.500A) Processing helix chain 'su' and resid 81 through 85 Processing helix chain 'su' and resid 102 through 118 removed outlier: 4.104A pdb=" N THRsu 106 " --> pdb=" O ASNsu 102 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILEsu 112 " --> pdb=" O LEUsu 108 " (cutoff:3.500A) Processing helix chain 'su' and resid 120 through 128 Processing helix chain 'sv' and resid 6 through 10 removed outlier: 3.558A pdb=" N ASPsv 9 " --> pdb=" O ASNsv 6 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VALsv 10 " --> pdb=" O ILEsv 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'sv' and resid 6 through 10' Processing helix chain 'sv' and resid 11 through 27 removed outlier: 3.673A pdb=" N GLUsv 21 " --> pdb=" O LYSsv 17 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HISsv 22 " --> pdb=" O ALAsv 18 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUsv 23 " --> pdb=" O TYRsv 19 " (cutoff:3.500A) Processing helix chain 'sv' and resid 52 through 68 removed outlier: 3.598A pdb=" N ILEsv 56 " --> pdb=" O ASPsv 52 " (cutoff:3.500A) Processing helix chain 'sv' and resid 72 through 80 Processing helix chain 'sv' and resid 97 through 111 removed outlier: 3.683A pdb=" N ASNsv 101 " --> pdb=" O SERsv 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYSsv 110 " --> pdb=" O GLNsv 106 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N METsv 111 " --> pdb=" O GLNsv 107 " (cutoff:3.500A) Processing helix chain 'sv' and resid 124 through 146 removed outlier: 3.610A pdb=" N GLNsv 137 " --> pdb=" O LYSsv 133 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALAsv 144 " --> pdb=" O LYSsv 140 " (cutoff:3.500A) Processing helix chain 'sv' and resid 148 through 152 Processing helix chain 'sw' and resid 28 through 45 removed outlier: 4.387A pdb=" N LYSsw 45 " --> pdb=" O GLUsw 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'sA' and resid 97 through 102 removed outlier: 6.842A pdb=" N THRsA 110 " --> pdb=" O PROsA 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'sD' and resid 55 through 58 removed outlier: 7.128A pdb=" N ARGsD 32 " --> pdb=" O THRsD 16 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILEsD 18 " --> pdb=" O GLNsD 30 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLNsD 30 " --> pdb=" O ILEsD 18 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLYsD 20 " --> pdb=" O VALsD 28 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VALsD 28 " --> pdb=" O GLYsD 20 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N ALAsg 140 " --> pdb=" O LEUsD 43 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASNsD 45 " --> pdb=" O ALAsg 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'sG' and resid 20 through 24 removed outlier: 6.632A pdb=" N GLYsG 36 " --> pdb=" O THRsG 21 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILEsG 23 " --> pdb=" O VALsG 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VALsG 34 " --> pdb=" O ILEsG 23 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSsG 62 " --> pdb=" O VALsG 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'sG' and resid 74 through 76 removed outlier: 3.553A pdb=" N ARGsG 93 " --> pdb=" O SERsG 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARGsG 104 " --> pdb=" O LEUsG 94 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASPsG 96 " --> pdb=" O SERsG 102 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SERsG 102 " --> pdb=" O ASPsG 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'sG' and resid 113 through 119 removed outlier: 4.288A pdb=" N ALAsG 145 " --> pdb=" O LEUsG 136 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASNsG 138 " --> pdb=" O CYSsG 143 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYSsG 143 " --> pdb=" O ASNsG 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'sG' and resid 156 through 160 Processing sheet with id=AA7, first strand: chain 'sd' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'sd' and resid 162 through 169 removed outlier: 3.842A pdb=" N GLYsd 147 " --> pdb=" O METsd 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'sl' and resid 21 through 24 Processing sheet with id=AB1, first strand: chain 'sq' and resid 92 through 96 Processing sheet with id=AB2, first strand: chain 'ss' and resid 21 through 22 Processing sheet with id=AB3, first strand: chain 'ss' and resid 21 through 22 removed outlier: 6.326A pdb=" N ARGss 45 " --> pdb=" O ILEss 82 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VALss 84 " --> pdb=" O ARGss 45 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'su' and resid 13 through 16 Processing sheet with id=AB5, first strand: chain 'sv' and resid 83 through 84 removed outlier: 3.568A pdb=" N HISsv 92 " --> pdb=" O TYRsv 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'sw' and resid 51 through 66 removed outlier: 8.701A pdb=" N SERsw 90 " --> pdb=" O PROsw 53 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARGsw 55 " --> pdb=" O VALsw 88 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VALsw 88 " --> pdb=" O ARGsw 55 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYSsw 86 " --> pdb=" O PROsw 57 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 302 hydrogen bonds 480 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.50: 15770 1.50 - 1.81: 8073 1.81 - 2.11: 8 2.11 - 2.42: 0 2.42 - 2.72: 1 Bond restraints: 23852 Sorted by residual: bond pdb=" O3' Asa1396 " pdb=" P Asa1425 " ideal model delta sigma weight residual 1.607 2.722 -1.115 1.20e-02 6.94e+03 8.64e+03 bond pdb=" O3' Usa1585 " pdb=" P Usa1586 " ideal model delta sigma weight residual 1.607 1.436 0.171 1.20e-02 6.94e+03 2.04e+02 bond pdb=" O3' Asa1508 " pdb=" P Gsa1509 " ideal model delta sigma weight residual 1.607 1.502 0.105 1.20e-02 6.94e+03 7.68e+01 bond pdb=" O3' Csa1789 " pdb=" P Csa1790 " ideal model delta sigma weight residual 1.607 1.503 0.104 1.20e-02 6.94e+03 7.53e+01 bond pdb=" O3' Usa1787 " pdb=" P Gsa1788 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.20e-02 6.94e+03 7.34e+01 ... (remaining 23847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.13: 34426 12.13 - 24.26: 14 24.26 - 36.39: 5 36.39 - 48.53: 2 48.53 - 60.66: 1 Bond angle restraints: 34448 Sorted by residual: angle pdb=" O3' Asa1396 " pdb=" P Asa1425 " pdb=" OP1 Asa1425 " ideal model delta sigma weight residual 108.00 168.66 -60.66 3.00e+00 1.11e-01 4.09e+02 angle pdb=" O3' Asa1396 " pdb=" P Asa1425 " pdb=" O5' Asa1425 " ideal model delta sigma weight residual 104.00 75.12 28.88 1.90e+00 2.77e-01 2.31e+02 angle pdb=" O3' Asa1396 " pdb=" P Asa1425 " pdb=" OP2 Asa1425 " ideal model delta sigma weight residual 108.00 64.36 43.64 3.00e+00 1.11e-01 2.12e+02 angle pdb=" O2' Usa1586 " pdb=" C2' Usa1586 " pdb=" C1' Usa1586 " ideal model delta sigma weight residual 110.60 71.08 39.52 3.00e+00 1.11e-01 1.74e+02 angle pdb=" O2' Gsa1509 " pdb=" C2' Gsa1509 " pdb=" C1' Gsa1509 " ideal model delta sigma weight residual 110.60 77.83 32.77 3.00e+00 1.11e-01 1.19e+02 ... (remaining 34443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 13463 35.61 - 71.21: 1307 71.21 - 106.82: 117 106.82 - 142.42: 13 142.42 - 178.03: 17 Dihedral angle restraints: 14917 sinusoidal: 10446 harmonic: 4471 Sorted by residual: dihedral pdb=" O4' Csa1563 " pdb=" C1' Csa1563 " pdb=" N1 Csa1563 " pdb=" C2 Csa1563 " ideal model delta sinusoidal sigma weight residual 200.00 30.11 169.89 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' Csa1383 " pdb=" C1' Csa1383 " pdb=" N1 Csa1383 " pdb=" C2 Csa1383 " ideal model delta sinusoidal sigma weight residual 200.00 30.65 169.35 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' Usa1271 " pdb=" C1' Usa1271 " pdb=" N1 Usa1271 " pdb=" C2 Usa1271 " ideal model delta sinusoidal sigma weight residual -160.00 5.59 -165.59 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 14914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3565 0.086 - 0.172: 673 0.172 - 0.258: 33 0.258 - 0.344: 12 0.344 - 0.429: 3 Chirality restraints: 4286 Sorted by residual: chirality pdb=" P Usa1586 " pdb=" OP1 Usa1586 " pdb=" OP2 Usa1586 " pdb=" O5' Usa1586 " both_signs ideal model delta sigma weight residual True 2.41 -1.98 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C2' Usa1596 " pdb=" C3' Usa1596 " pdb=" O2' Usa1596 " pdb=" C1' Usa1596 " both_signs ideal model delta sigma weight residual False -2.62 -2.98 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C2' Usa1589 " pdb=" C3' Usa1589 " pdb=" O2' Usa1589 " pdb=" C1' Usa1589 " both_signs ideal model delta sigma weight residual False -2.62 -2.96 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 4283 not shown) Planarity restraints: 2559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' Csa1791 " 0.075 2.00e-02 2.50e+03 3.56e-02 2.86e+01 pdb=" N1 Csa1791 " -0.017 2.00e-02 2.50e+03 pdb=" C2 Csa1791 " -0.019 2.00e-02 2.50e+03 pdb=" O2 Csa1791 " -0.028 2.00e-02 2.50e+03 pdb=" N3 Csa1791 " 0.005 2.00e-02 2.50e+03 pdb=" C4 Csa1791 " -0.001 2.00e-02 2.50e+03 pdb=" N4 Csa1791 " 0.048 2.00e-02 2.50e+03 pdb=" C5 Csa1791 " -0.025 2.00e-02 2.50e+03 pdb=" C6 Csa1791 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' Asa1669 " -0.069 2.00e-02 2.50e+03 3.02e-02 2.50e+01 pdb=" N9 Asa1669 " 0.064 2.00e-02 2.50e+03 pdb=" C8 Asa1669 " 0.002 2.00e-02 2.50e+03 pdb=" N7 Asa1669 " 0.009 2.00e-02 2.50e+03 pdb=" C5 Asa1669 " 0.001 2.00e-02 2.50e+03 pdb=" C6 Asa1669 " -0.010 2.00e-02 2.50e+03 pdb=" N6 Asa1669 " -0.020 2.00e-02 2.50e+03 pdb=" N1 Asa1669 " -0.012 2.00e-02 2.50e+03 pdb=" C2 Asa1669 " 0.009 2.00e-02 2.50e+03 pdb=" N3 Asa1669 " 0.018 2.00e-02 2.50e+03 pdb=" C4 Asa1669 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' Gsa1509 " 0.065 2.00e-02 2.50e+03 2.72e-02 2.22e+01 pdb=" N9 Gsa1509 " -0.056 2.00e-02 2.50e+03 pdb=" C8 Gsa1509 " -0.002 2.00e-02 2.50e+03 pdb=" N7 Gsa1509 " 0.002 2.00e-02 2.50e+03 pdb=" C5 Gsa1509 " -0.009 2.00e-02 2.50e+03 pdb=" C6 Gsa1509 " 0.012 2.00e-02 2.50e+03 pdb=" O6 Gsa1509 " 0.023 2.00e-02 2.50e+03 pdb=" N1 Gsa1509 " -0.003 2.00e-02 2.50e+03 pdb=" C2 Gsa1509 " -0.003 2.00e-02 2.50e+03 pdb=" N2 Gsa1509 " 0.007 2.00e-02 2.50e+03 pdb=" N3 Gsa1509 " -0.012 2.00e-02 2.50e+03 pdb=" C4 Gsa1509 " -0.023 2.00e-02 2.50e+03 ... (remaining 2556 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 534 2.62 - 3.19: 19111 3.19 - 3.76: 39768 3.76 - 4.33: 54341 4.33 - 4.90: 80615 Nonbonded interactions: 194369 Sorted by model distance: nonbonded pdb=" N2 Gsa1750 " pdb=" O2' Gsa1776 " model vdw 2.052 3.120 nonbonded pdb=" O2' Csa1441 " pdb=" O5' Asa1442 " model vdw 2.070 3.040 nonbonded pdb=" O2' Asa1669 " pdb=" O5' Asa1670 " model vdw 2.102 3.040 nonbonded pdb=" OD1 ASNsd 36 " pdb=" OH TYRsd 48 " model vdw 2.120 3.040 nonbonded pdb=" OP2 Usa1308 " pdb=" O2' Csa1309 " model vdw 2.134 3.040 ... (remaining 194364 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: 0.870 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.010 1.115 23853 Z= 0.799 Angle : 1.111 60.656 34450 Z= 0.717 Chirality : 0.063 0.429 4286 Planarity : 0.005 0.061 2559 Dihedral : 23.073 178.025 12016 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.41 % Favored : 92.26 % Rotamer: Outliers : 4.77 % Allowed : 36.59 % Favored : 58.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.23 (0.22), residues: 1498 helix: -0.33 (0.22), residues: 523 sheet: -0.42 (0.36), residues: 239 loop : -1.26 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGsd 54 TYR 0.013 0.001 TYRsE 7 PHE 0.032 0.002 PHEsd 2 TRP 0.004 0.001 TRPsA 107 HIS 0.006 0.001 HISsG 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00970 / 0.80 (23852) covalent geometry : angle 1.11072 / 0.72 (34448) SS BOND : bond 0.00539 / 0.28 ( 1) SS BOND : angle 1.18414 / 0.68 ( 2) hydrogen bonds : bond 0.23026 / 15.46 ( 787) hydrogen bonds : angle 7.60333 / 5.38 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sA 65 MET cc_start: 0.7620 (mtp) cc_final: 0.7357 (mtp) REVERT: sG 301 HIS cc_start: 0.7676 (m90) cc_final: 0.7436 (m90) REVERT: sd 34 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: sd 48 TYR cc_start: 0.5554 (p90) cc_final: 0.5311 (p90) REVERT: sl 2 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7279 (tpp80) REVERT: sq 110 MET cc_start: 0.8358 (ptp) cc_final: 0.8076 (ptp) REVERT: ss 43 MET cc_start: 0.8046 (mmt) cc_final: 0.7563 (mmt) REVERT: su 126 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.6573 (m170) REVERT: sv 152 MET cc_start: 0.6650 (ttp) cc_final: 0.6421 (ttp) REVERT: sw 116 MET cc_start: 0.6678 (tpp) cc_final: 0.6032 (tpp) outliers start: 64 outliers final: 39 residues processed: 284 average time/residue: 0.1384 time to fit residues: 62.4901 Evaluate side-chains 250 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sE residue 56 ASP Chi-restraints excluded: chain sG residue 13 LEU Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 172 SER Chi-restraints excluded: chain sG residue 306 ILE Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 34 GLU Chi-restraints excluded: chain sd residue 67 THR Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sq residue 66 THR Chi-restraints excluded: chain sq residue 104 VAL Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 97 SER Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 94 THR Chi-restraints excluded: chain sv residue 100 VAL Chi-restraints excluded: chain sw residue 19 ASN Chi-restraints excluded: chain sw residue 25 THR Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 38 GLU Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 91 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0040 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0050 overall best weight: 4.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sg 22 ASN sg 67 GLN sl 31 HIS ss 47 ASN ss 89 GLN su 73 ASN sw 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.084094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073036 restraints weight = 70426.179| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.64 r_work: 0.3341 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23853 Z= 0.174 Angle : 0.647 9.082 34450 Z= 0.356 Chirality : 0.045 0.448 4286 Planarity : 0.005 0.063 2559 Dihedral : 22.915 178.373 8966 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.81 % Favored : 93.86 % Rotamer: Outliers : 7.60 % Allowed : 32.27 % Favored : 60.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.87 (0.21), residues: 1498 helix: 0.28 (0.22), residues: 519 sheet: -0.30 (0.35), residues: 244 loop : -1.27 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGsd 54 TYR 0.017 0.002 TYRsd 48 PHE 0.020 0.002 PHEsd 2 TRP 0.008 0.001 TRPsG 175 HIS 0.006 0.001 HISsg 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (23852) covalent geometry : angle 0.64684 / 0.36 (34448) SS BOND : bond 0.00360 / 0.19 ( 1) SS BOND : angle 0.65454 / 0.38 ( 2) hydrogen bonds : bond 0.07410 / 4.97 ( 787) hydrogen bonds : angle 4.78319 / 3.36 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 233 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sA 65 MET cc_start: 0.7792 (mtp) cc_final: 0.7423 (mtp) REVERT: sd 203 MET cc_start: 0.8505 (ttp) cc_final: 0.8299 (ttt) REVERT: sg 41 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8518 (mp) REVERT: sl 2 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6928 (tpt-90) REVERT: sq 110 MET cc_start: 0.8467 (ptp) cc_final: 0.8122 (ptp) REVERT: ss 43 MET cc_start: 0.8204 (mmt) cc_final: 0.7513 (mmt) REVERT: ss 114 GLU cc_start: 0.8138 (tp30) cc_final: 0.7681 (tp30) REVERT: su 126 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.6344 (m170) REVERT: sv 126 GLU cc_start: 0.8718 (pm20) cc_final: 0.8511 (pm20) REVERT: sw 38 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8231 (tm-30) outliers start: 102 outliers final: 60 residues processed: 308 average time/residue: 0.1447 time to fit residues: 72.0117 Evaluate side-chains 267 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 61 GLU Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 91 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 58 LEU Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sG residue 13 LEU Chi-restraints excluded: chain sG residue 69 HIS Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 306 ILE Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 86 LEU Chi-restraints excluded: chain sd residue 104 LYS Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 149 GLU Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 41 ILE Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sq residue 20 SER Chi-restraints excluded: chain sq residue 21 LEU Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 82 LYS Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 8 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 97 SER Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 94 THR Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sw residue 24 ILE Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 38 GLU Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 68 THR Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 40.0000 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sg 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.072953 restraints weight = 70231.066| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.59 r_work: 0.3338 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 23853 Z= 0.168 Angle : 0.593 8.612 34450 Z= 0.330 Chirality : 0.043 0.452 4286 Planarity : 0.005 0.065 2559 Dihedral : 22.795 178.734 8948 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.87 % Favored : 93.79 % Rotamer: Outliers : 7.38 % Allowed : 32.12 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.68 (0.21), residues: 1498 helix: 0.61 (0.22), residues: 527 sheet: -0.28 (0.35), residues: 244 loop : -1.30 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGss 45 TYR 0.013 0.002 TYRsv 139 PHE 0.017 0.001 PHEsd 2 TRP 0.008 0.001 TRPsG 95 HIS 0.004 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (23852) covalent geometry : angle 0.59295 / 0.33 (34448) SS BOND : bond 0.00350 / 0.18 ( 1) SS BOND : angle 0.64526 / 0.38 ( 2) hydrogen bonds : bond 0.06795 / 4.58 ( 787) hydrogen bonds : angle 4.41522 / 3.09 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 219 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sG 200 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5458 (m-10) REVERT: sG 301 HIS cc_start: 0.7616 (m90) cc_final: 0.7378 (m90) REVERT: sg 46 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8409 (mtmm) REVERT: sl 2 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.6864 (tpt-90) REVERT: sq 110 MET cc_start: 0.8585 (ptp) cc_final: 0.8253 (ptp) REVERT: ss 43 MET cc_start: 0.8438 (mmt) cc_final: 0.7854 (mmt) REVERT: ss 114 GLU cc_start: 0.8201 (tp30) cc_final: 0.7911 (tp30) REVERT: su 126 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.6474 (m90) REVERT: sv 126 GLU cc_start: 0.8716 (pm20) cc_final: 0.8514 (pm20) REVERT: sw 116 MET cc_start: 0.6706 (tpp) cc_final: 0.5951 (tpp) outliers start: 99 outliers final: 68 residues processed: 292 average time/residue: 0.1361 time to fit residues: 63.1528 Evaluate side-chains 269 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sA residue 91 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 25 ARG Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sE residue 37 ASP Chi-restraints excluded: chain sG residue 13 LEU Chi-restraints excluded: chain sG residue 69 HIS Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 103 VAL Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 200 PHE Chi-restraints excluded: chain sG residue 306 ILE Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 86 LEU Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 149 GLU Chi-restraints excluded: chain sd residue 171 MET Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 46 LYS Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 125 GLU Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 66 THR Chi-restraints excluded: chain sq residue 20 SER Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 97 SER Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 94 THR Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 118 GLN Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 146 VAL Chi-restraints excluded: chain sw residue 25 THR Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 68 THR Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 28 optimal weight: 30.0000 chunk 179 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sG 109 HIS sd 115 GLN sg 22 ASN sg 67 GLN sl 40 GLN ss 47 ASN ss 108 ASN su 54 ASN sw 42 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071520 restraints weight = 70613.904| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.61 r_work: 0.3306 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23853 Z= 0.215 Angle : 0.666 19.790 34450 Z= 0.360 Chirality : 0.046 0.461 4286 Planarity : 0.005 0.065 2559 Dihedral : 22.782 179.218 8944 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.08 % Favored : 92.59 % Rotamer: Outliers : 8.12 % Allowed : 31.07 % Favored : 60.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.88 (0.21), residues: 1498 helix: 0.52 (0.22), residues: 523 sheet: -0.45 (0.34), residues: 247 loop : -1.45 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGsD 32 TYR 0.018 0.002 TYRsv 66 PHE 0.022 0.002 PHEsd 2 TRP 0.010 0.001 TRPsG 95 HIS 0.008 0.002 HISsG 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (23852) covalent geometry : angle 0.66579 / 0.36 (34448) SS BOND : bond 0.00623 / 0.33 ( 1) SS BOND : angle 1.56673 / 0.91 ( 2) hydrogen bonds : bond 0.06921 / 4.68 ( 787) hydrogen bonds : angle 4.26217 / 2.96 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 214 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sA 65 MET cc_start: 0.7571 (mtm) cc_final: 0.7348 (mtt) REVERT: sG 81 GLN cc_start: 0.8122 (pp30) cc_final: 0.7083 (pp30) REVERT: sG 95 TRP cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (m100) REVERT: sG 96 ASP cc_start: 0.7857 (p0) cc_final: 0.7538 (p0) REVERT: sG 132 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8653 (mtmm) REVERT: sG 200 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: sd 21 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8514 (mmp-170) REVERT: sd 141 MET cc_start: 0.8339 (mmm) cc_final: 0.8124 (tpt) REVERT: sl 2 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7075 (tpp80) REVERT: sq 110 MET cc_start: 0.8599 (ptp) cc_final: 0.8242 (ptp) REVERT: ss 27 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8146 (ttmt) REVERT: ss 38 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8031 (ttmm) REVERT: ss 43 MET cc_start: 0.8374 (mmt) cc_final: 0.7799 (mmt) REVERT: ss 47 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8431 (m110) REVERT: ss 114 GLU cc_start: 0.8187 (tp30) cc_final: 0.7852 (tp30) REVERT: su 107 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8577 (mmt-90) REVERT: su 126 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.6506 (m90) REVERT: sw 80 TYR cc_start: 0.8395 (m-10) cc_final: 0.8111 (m-10) outliers start: 109 outliers final: 76 residues processed: 298 average time/residue: 0.1401 time to fit residues: 66.1711 Evaluate side-chains 282 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sG residue 13 LEU Chi-restraints excluded: chain sG residue 69 HIS Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 95 TRP Chi-restraints excluded: chain sG residue 103 VAL Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 133 THR Chi-restraints excluded: chain sG residue 200 PHE Chi-restraints excluded: chain sG residue 306 ILE Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 21 ARG Chi-restraints excluded: chain sd residue 67 THR Chi-restraints excluded: chain sd residue 86 LEU Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 178 THR Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 22 ASN Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 95 VAL Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sq residue 20 SER Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 66 THR Chi-restraints excluded: chain sq residue 74 LEU Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 27 LYS Chi-restraints excluded: chain ss residue 28 LYS Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain st residue 61 ILE Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 99 LEU Chi-restraints excluded: chain su residue 107 ARG Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 94 THR Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 118 GLN Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 146 VAL Chi-restraints excluded: chain sw residue 25 THR Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 68 THR Chi-restraints excluded: chain sw residue 92 LYS Chi-restraints excluded: chain sw residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 147 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 142 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sg 22 ASN su 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.082731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071728 restraints weight = 70035.972| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.58 r_work: 0.3310 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23853 Z= 0.200 Angle : 0.622 9.147 34450 Z= 0.341 Chirality : 0.045 0.454 4286 Planarity : 0.005 0.065 2559 Dihedral : 22.777 178.703 8941 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.88 % Favored : 92.79 % Rotamer: Outliers : 7.53 % Allowed : 31.97 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.80 (0.21), residues: 1498 helix: 0.61 (0.22), residues: 528 sheet: -0.42 (0.34), residues: 247 loop : -1.44 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsG 130 TYR 0.014 0.002 TYRsv 66 PHE 0.025 0.002 PHEsd 2 TRP 0.007 0.001 TRPsG 95 HIS 0.006 0.001 HISsg 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 (23852) covalent geometry : angle 0.62227 / 0.34 (34448) SS BOND : bond 0.00577 / 0.30 ( 1) SS BOND : angle 0.93175 / 0.52 ( 2) hydrogen bonds : bond 0.06701 / 4.52 ( 787) hydrogen bonds : angle 4.19631 / 2.92 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 208 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sG 81 GLN cc_start: 0.8160 (pp30) cc_final: 0.6954 (pp30) REVERT: sG 132 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8625 (mtmm) REVERT: sd 98 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6223 (tp) REVERT: sl 2 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7225 (tpp80) REVERT: sl 11 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7092 (mp) REVERT: sq 110 MET cc_start: 0.8612 (ptp) cc_final: 0.8221 (ptp) REVERT: ss 43 MET cc_start: 0.8535 (mmt) cc_final: 0.7945 (mmt) REVERT: ss 47 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: ss 89 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8067 (mm110) REVERT: ss 114 GLU cc_start: 0.8190 (tp30) cc_final: 0.7890 (tp30) REVERT: su 126 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.6522 (m90) REVERT: sw 75 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7986 (mmtt) outliers start: 101 outliers final: 71 residues processed: 287 average time/residue: 0.1324 time to fit residues: 60.5778 Evaluate side-chains 280 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 201 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 103 VAL Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 86 LEU Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 153 SER Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 11 ILE Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 74 LEU Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 28 LYS Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 58 VAL Chi-restraints excluded: chain ss residue 63 VAL Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain ss residue 89 GLN Chi-restraints excluded: chain ss residue 125 LEU Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 54 ASN Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 106 THR Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 130 LEU Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 94 THR Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 146 VAL Chi-restraints excluded: chain sw residue 25 THR Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 chunk 178 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ss 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.083083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072116 restraints weight = 70445.359| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.60 r_work: 0.3318 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23853 Z= 0.173 Angle : 0.594 9.536 34450 Z= 0.328 Chirality : 0.043 0.440 4286 Planarity : 0.004 0.063 2559 Dihedral : 22.769 178.584 8937 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.94 % Favored : 92.72 % Rotamer: Outliers : 7.38 % Allowed : 32.19 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.70 (0.21), residues: 1498 helix: 0.72 (0.22), residues: 527 sheet: -0.30 (0.34), residues: 240 loop : -1.41 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGsu 145 TYR 0.022 0.002 TYRsv 66 PHE 0.025 0.001 PHEsd 2 TRP 0.007 0.001 TRPsG 95 HIS 0.006 0.001 HISsg 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (23852) covalent geometry : angle 0.59415 / 0.33 (34448) SS BOND : bond 0.00454 / 0.24 ( 1) SS BOND : angle 0.89330 / 0.49 ( 2) hydrogen bonds : bond 0.06447 / 4.35 ( 787) hydrogen bonds : angle 4.10428 / 2.84 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 214 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sG 81 GLN cc_start: 0.8185 (pp30) cc_final: 0.6944 (pp30) REVERT: sG 95 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.8176 (m100) REVERT: sG 109 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6388 (t-90) REVERT: sG 132 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8722 (mtmm) REVERT: sd 98 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6237 (tp) REVERT: sg 125 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: sl 2 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7184 (tpp80) REVERT: ss 38 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8378 (ttmm) REVERT: ss 43 MET cc_start: 0.8484 (mmt) cc_final: 0.8041 (mmt) REVERT: ss 47 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8341 (m110) REVERT: ss 114 GLU cc_start: 0.8217 (tp30) cc_final: 0.7908 (tp30) REVERT: su 126 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.6498 (m90) REVERT: sw 75 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7991 (mmtt) REVERT: sw 80 TYR cc_start: 0.8353 (m-10) cc_final: 0.8106 (m-10) REVERT: sw 92 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7523 (mmmm) outliers start: 99 outliers final: 71 residues processed: 291 average time/residue: 0.1345 time to fit residues: 62.0681 Evaluate side-chains 288 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 206 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 84 ILE Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 95 TRP Chi-restraints excluded: chain sG residue 103 VAL Chi-restraints excluded: chain sG residue 109 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 133 THR Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 67 THR Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 125 GLU Chi-restraints excluded: chain sg residue 126 ASP Chi-restraints excluded: chain sg residue 158 MET Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 74 LEU Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 109 GLU Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 28 LYS Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 58 VAL Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 37 CYS Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 130 LEU Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 118 GLN Chi-restraints excluded: chain sv residue 125 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 146 VAL Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Chi-restraints excluded: chain sw residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 42 optimal weight: 40.0000 chunk 132 optimal weight: 8.9990 chunk 69 optimal weight: 30.0000 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sG 248 GLN ss 47 ASN ss 89 GLN su 54 ASN sw 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.073697 restraints weight = 69823.205| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.60 r_work: 0.3357 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23853 Z= 0.120 Angle : 0.549 10.297 34450 Z= 0.308 Chirality : 0.040 0.408 4286 Planarity : 0.004 0.062 2559 Dihedral : 22.750 178.694 8936 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.21 % Favored : 93.52 % Rotamer: Outliers : 7.15 % Allowed : 32.41 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.47 (0.22), residues: 1498 helix: 0.97 (0.22), residues: 526 sheet: -0.21 (0.34), residues: 238 loop : -1.31 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsG 104 TYR 0.018 0.001 TYRsv 66 PHE 0.021 0.001 PHEsd 2 TRP 0.010 0.001 TRPsG 95 HIS 0.004 0.001 HISsg 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (23852) covalent geometry : angle 0.54881 / 0.31 (34448) SS BOND : bond 0.00093 / 0.05 ( 1) SS BOND : angle 0.71944 / 0.38 ( 2) hydrogen bonds : bond 0.05959 / 4.02 ( 787) hydrogen bonds : angle 3.94085 / 2.72 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 209 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sE 28 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8238 (ptmt) REVERT: sG 81 GLN cc_start: 0.8207 (pp30) cc_final: 0.6975 (pp30) REVERT: sG 132 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: sd 34 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8217 (tp30) REVERT: sd 98 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6171 (tp) REVERT: sg 26 TYR cc_start: 0.8806 (m-80) cc_final: 0.8445 (m-80) REVERT: sl 2 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7143 (tpt170) REVERT: ss 43 MET cc_start: 0.8424 (mmt) cc_final: 0.7987 (mmt) REVERT: ss 47 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8498 (m110) REVERT: ss 114 GLU cc_start: 0.8171 (tp30) cc_final: 0.7874 (tp30) REVERT: su 107 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8541 (mmt-90) REVERT: su 126 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.6559 (m90) REVERT: sw 33 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8121 (mm-30) REVERT: sw 44 LYS cc_start: 0.8417 (mptt) cc_final: 0.8176 (mmtm) REVERT: sw 75 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8027 (mmtt) REVERT: sw 80 TYR cc_start: 0.8314 (m-10) cc_final: 0.8049 (m-10) REVERT: sw 92 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7583 (mmmm) outliers start: 96 outliers final: 66 residues processed: 285 average time/residue: 0.1426 time to fit residues: 65.1633 Evaluate side-chains 277 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 36 MET Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 28 LYS Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sG residue 69 HIS Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sG residue 153 SER Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 34 GLU Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 104 LYS Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 178 THR Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 125 GLU Chi-restraints excluded: chain sg residue 126 ASP Chi-restraints excluded: chain sg residue 158 MET Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 104 VAL Chi-restraints excluded: chain sq residue 109 GLU Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 28 LYS Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain ss residue 125 LEU Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 107 ARG Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 130 LEU Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 125 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 146 VAL Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 64 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 79 optimal weight: 30.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ss 47 ASN su 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.073797 restraints weight = 71422.100| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.52 r_work: 0.3359 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23853 Z= 0.273 Angle : 0.713 11.032 34450 Z= 0.377 Chirality : 0.050 0.450 4286 Planarity : 0.005 0.062 2559 Dihedral : 22.756 178.642 8931 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.08 % Favored : 91.66 % Rotamer: Outliers : 7.75 % Allowed : 31.97 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.91 (0.21), residues: 1498 helix: 0.68 (0.22), residues: 522 sheet: -0.62 (0.33), residues: 247 loop : -1.56 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGsG 130 TYR 0.023 0.002 TYRsv 66 PHE 0.030 0.002 PHEsd 2 TRP 0.005 0.001 TRPsG 137 HIS 0.007 0.002 HISsg 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.27 (23852) covalent geometry : angle 0.71245 / 0.38 (34448) SS BOND : bond 0.00984 / 0.52 ( 1) SS BOND : angle 1.43642 / 0.79 ( 2) hydrogen bonds : bond 0.07284 / 4.93 ( 787) hydrogen bonds : angle 4.19674 / 2.92 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 199 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sE 28 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8378 (ptmt) REVERT: sE 42 CYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7026 (m) REVERT: sG 109 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6518 (t-90) REVERT: sG 132 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8796 (mtmm) REVERT: sd 21 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8642 (mmp-170) REVERT: sd 98 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6573 (tp) REVERT: sl 2 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7510 (tpp80) REVERT: ss 43 MET cc_start: 0.8467 (mmt) cc_final: 0.7873 (mmt) REVERT: ss 47 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8422 (m110) REVERT: ss 114 GLU cc_start: 0.8184 (tp30) cc_final: 0.7848 (tp30) REVERT: st 67 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6839 (mmm-85) REVERT: su 107 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8642 (mmt-90) REVERT: su 126 HIS cc_start: 0.8886 (OUTLIER) cc_final: 0.6773 (m90) REVERT: sw 33 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8230 (mm-30) REVERT: sw 75 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8051 (mmtt) REVERT: sw 92 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7825 (mmmm) outliers start: 104 outliers final: 78 residues processed: 281 average time/residue: 0.1391 time to fit residues: 61.9361 Evaluate side-chains 281 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 191 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 36 MET Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 28 LYS Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sE residue 42 CYS Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 109 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sG residue 153 SER Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 21 ARG Chi-restraints excluded: chain sd residue 67 THR Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 153 SER Chi-restraints excluded: chain sd residue 178 THR Chi-restraints excluded: chain sd residue 180 GLN Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sd residue 221 VAL Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 95 VAL Chi-restraints excluded: chain sg residue 126 ASP Chi-restraints excluded: chain sg residue 158 MET Chi-restraints excluded: chain sg residue 171 LEU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sl residue 48 LEU Chi-restraints excluded: chain sq residue 21 LEU Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 66 THR Chi-restraints excluded: chain sq residue 74 LEU Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 104 VAL Chi-restraints excluded: chain sq residue 109 GLU Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 47 ASN Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 63 VAL Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain ss residue 85 THR Chi-restraints excluded: chain ss residue 125 LEU Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 54 ASN Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 104 VAL Chi-restraints excluded: chain su residue 106 THR Chi-restraints excluded: chain su residue 107 ARG Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 125 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sw residue 25 THR Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 2.9990 chunk 59 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 chunk 193 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 overall best weight: 4.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** sg 81 HIS ** su 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.085336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.074644 restraints weight = 71154.506| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.55 r_work: 0.3417 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23853 Z= 0.154 Angle : 0.593 10.850 34450 Z= 0.328 Chirality : 0.042 0.401 4286 Planarity : 0.004 0.062 2559 Dihedral : 22.788 179.623 8931 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.74 % Favored : 92.99 % Rotamer: Outliers : 6.56 % Allowed : 33.01 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.66 (0.21), residues: 1498 helix: 0.83 (0.22), residues: 526 sheet: -0.31 (0.34), residues: 233 loop : -1.44 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsd 54 TYR 0.018 0.002 TYRsv 66 PHE 0.026 0.001 PHEsd 2 TRP 0.004 0.001 TRPsG 95 HIS 0.004 0.001 HISsu 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (23852) covalent geometry : angle 0.59277 / 0.33 (34448) SS BOND : bond 0.00335 / 0.18 ( 1) SS BOND : angle 0.90171 / 0.50 ( 2) hydrogen bonds : bond 0.06307 / 4.25 ( 787) hydrogen bonds : angle 4.03220 / 2.79 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 199 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sE 28 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8295 (ptmt) REVERT: sG 81 GLN cc_start: 0.8253 (pp30) cc_final: 0.7955 (pp30) REVERT: sG 109 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6406 (t-90) REVERT: sG 132 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8775 (mtmm) REVERT: sd 98 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6364 (tp) REVERT: sl 2 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7333 (tpp80) REVERT: sq 110 MET cc_start: 0.8485 (ptm) cc_final: 0.8131 (ptp) REVERT: ss 43 MET cc_start: 0.8394 (mmt) cc_final: 0.7933 (mmt) REVERT: ss 114 GLU cc_start: 0.8177 (tp30) cc_final: 0.7865 (tp30) REVERT: st 67 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6889 (mmm-85) REVERT: su 126 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.6593 (m90) REVERT: sw 33 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8151 (mm-30) REVERT: sw 75 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8071 (mmtt) REVERT: sw 80 TYR cc_start: 0.8449 (m-10) cc_final: 0.8190 (m-10) REVERT: sw 92 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7777 (mmmm) outliers start: 88 outliers final: 68 residues processed: 262 average time/residue: 0.1357 time to fit residues: 56.8132 Evaluate side-chains 270 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 194 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 36 MET Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 28 LYS Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 109 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 133 THR Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sG residue 153 SER Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 104 LYS Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 178 THR Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 126 ASP Chi-restraints excluded: chain sg residue 158 MET Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sl residue 48 LEU Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 66 THR Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 28 LYS Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain ss residue 85 THR Chi-restraints excluded: chain ss residue 125 LEU Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain st residue 69 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 125 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 52 optimal weight: 40.0000 chunk 90 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** sE 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** su 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.084853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074360 restraints weight = 71498.646| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.51 r_work: 0.3394 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23853 Z= 0.187 Angle : 0.622 11.265 34450 Z= 0.337 Chirality : 0.044 0.389 4286 Planarity : 0.005 0.060 2559 Dihedral : 22.757 178.842 8931 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.61 % Favored : 92.12 % Rotamer: Outliers : 6.11 % Allowed : 33.76 % Favored : 60.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.68 (0.21), residues: 1498 helix: 0.85 (0.22), residues: 526 sheet: -0.34 (0.34), residues: 233 loop : -1.47 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGsd 54 TYR 0.018 0.002 TYRsv 66 PHE 0.027 0.001 PHEsd 2 TRP 0.003 0.001 TRPsv 53 HIS 0.006 0.001 HISsg 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (23852) covalent geometry : angle 0.62155 / 0.34 (34448) SS BOND : bond 0.00596 / 0.31 ( 1) SS BOND : angle 1.04482 / 0.56 ( 2) hydrogen bonds : bond 0.06437 / 4.34 ( 787) hydrogen bonds : angle 4.03655 / 2.80 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sA 95 GLU cc_start: 0.8522 (mp0) cc_final: 0.8262 (mp0) REVERT: sE 28 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8340 (ptmt) REVERT: sE 42 CYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7080 (m) REVERT: sG 81 GLN cc_start: 0.8333 (pp30) cc_final: 0.7127 (pp30) REVERT: sG 109 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.6495 (t-90) REVERT: sG 132 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8832 (mtmm) REVERT: sd 98 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6459 (tp) REVERT: sl 2 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7467 (tpp80) REVERT: sq 110 MET cc_start: 0.8472 (ptm) cc_final: 0.8122 (ptp) REVERT: ss 43 MET cc_start: 0.8520 (mmt) cc_final: 0.7900 (mmt) REVERT: ss 114 GLU cc_start: 0.8196 (tp30) cc_final: 0.7885 (tp30) REVERT: st 67 ARG cc_start: 0.7269 (mtp180) cc_final: 0.6895 (mmm-85) REVERT: su 107 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8689 (mmt-90) REVERT: su 126 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.6677 (m90) REVERT: sw 33 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8246 (mm-30) REVERT: sw 75 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8052 (mmtt) REVERT: sw 80 TYR cc_start: 0.8483 (m-10) cc_final: 0.8228 (m-10) REVERT: sw 92 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7883 (mmmm) outliers start: 82 outliers final: 68 residues processed: 259 average time/residue: 0.1316 time to fit residues: 54.3369 Evaluate side-chains 270 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 192 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 44 LEU Chi-restraints excluded: chain sA residue 54 THR Chi-restraints excluded: chain sA residue 67 VAL Chi-restraints excluded: chain sA residue 88 LEU Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 VAL Chi-restraints excluded: chain sD residue 36 MET Chi-restraints excluded: chain sD residue 57 THR Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 4 TYR Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sE residue 28 LYS Chi-restraints excluded: chain sE residue 30 LEU Chi-restraints excluded: chain sE residue 42 CYS Chi-restraints excluded: chain sG residue 75 VAL Chi-restraints excluded: chain sG residue 90 HIS Chi-restraints excluded: chain sG residue 101 GLU Chi-restraints excluded: chain sG residue 109 HIS Chi-restraints excluded: chain sG residue 118 PHE Chi-restraints excluded: chain sG residue 132 LYS Chi-restraints excluded: chain sG residue 133 THR Chi-restraints excluded: chain sG residue 140 VAL Chi-restraints excluded: chain sG residue 153 SER Chi-restraints excluded: chain sd residue 2 PHE Chi-restraints excluded: chain sd residue 13 ASP Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 98 ILE Chi-restraints excluded: chain sd residue 133 VAL Chi-restraints excluded: chain sd residue 153 SER Chi-restraints excluded: chain sd residue 178 THR Chi-restraints excluded: chain sd residue 195 ILE Chi-restraints excluded: chain sd residue 201 THR Chi-restraints excluded: chain sd residue 206 THR Chi-restraints excluded: chain sg residue 49 VAL Chi-restraints excluded: chain sg residue 126 ASP Chi-restraints excluded: chain sg residue 158 MET Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 2 ARG Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 31 HIS Chi-restraints excluded: chain sl residue 48 LEU Chi-restraints excluded: chain sq residue 35 MET Chi-restraints excluded: chain sq residue 66 THR Chi-restraints excluded: chain sq residue 79 CYS Chi-restraints excluded: chain sq residue 89 ILE Chi-restraints excluded: chain sq residue 104 VAL Chi-restraints excluded: chain sq residue 115 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 55 ASN Chi-restraints excluded: chain ss residue 84 VAL Chi-restraints excluded: chain ss residue 85 THR Chi-restraints excluded: chain ss residue 125 LEU Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 5 ARG Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 32 LYS Chi-restraints excluded: chain st residue 40 VAL Chi-restraints excluded: chain st residue 54 ILE Chi-restraints excluded: chain su residue 13 MET Chi-restraints excluded: chain su residue 51 ILE Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 66 GLU Chi-restraints excluded: chain su residue 107 ARG Chi-restraints excluded: chain su residue 126 HIS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain su residue 139 THR Chi-restraints excluded: chain sv residue 36 ASP Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 117 ILE Chi-restraints excluded: chain sv residue 125 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sw residue 32 VAL Chi-restraints excluded: chain sw residue 48 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 75 LYS Chi-restraints excluded: chain sw residue 92 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 21 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 68 optimal weight: 30.0000 chunk 20 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 172 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... su 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.084564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.073851 restraints weight = 71216.451| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.54 r_work: 0.3398 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23853 Z= 0.198 Angle : 0.635 11.679 34450 Z= 0.344 Chirality : 0.045 0.389 4286 Planarity : 0.005 0.061 2559 Dihedral : 22.775 178.095 8931 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.08 % Favored : 92.66 % Rotamer: Outliers : 6.48 % Allowed : 33.53 % Favored : 59.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.71 (0.21), residues: 1498 helix: 0.83 (0.22), residues: 526 sheet: -0.34 (0.34), residues: 235 loop : -1.51 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGsd 54 TYR 0.019 0.002 TYRsv 66 PHE 0.029 0.001 PHEsd 2 TRP 0.003 0.001 TRPsv 53 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (23852) covalent geometry : angle 0.63500 / 0.34 (34448) SS BOND : bond 0.00600 / 0.32 ( 1) SS BOND : angle 1.04759 / 0.57 ( 2) hydrogen bonds : bond 0.06508 / 4.38 ( 787) hydrogen bonds : angle 4.05867 / 2.81 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.76 seconds wall clock time: 79 minutes 21.92 seconds (4761.92 seconds total)