Starting phenix.real_space_refine on Sat Oct 31 01:29:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.map" model { file = "/net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r92_4766/10_2026/6r92_4766.cif" } resolution = 4.8 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= 0.002 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: 6 Type Number sf(0) Gaussians P 288 5.49 5 S 66 5.16 5 C 12679 2.51 5 N 3869 2.21 5 O 4598 1.98 5 H 19035 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40535 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 4611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4611 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 4581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 4581 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "L" Number of atoms: 5642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5642 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 22, 'TRANS': 340} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1645 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1347 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1877 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "D" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1507 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1646 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1348 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1878 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "H" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1555 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "K" Number of atoms: 12898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 12898 Classifications: {'peptide': 825} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 797} Chain breaks: 1 Time building chain proxies: 6.83, per 1000 atoms: 0.17 Number of scatterers: 40535 At special positions: 0 Unit cell: (131.58, 179.74, 145.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 288 15.00 O 4598 8.00 N 3869 7.00 C 12679 6.00 H 19035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 944.8 milliseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3670 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 34 sheets defined 34.1% alpha, 26.1% beta 138 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 7.86 Creating SS restraints... Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 99 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.527A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.656A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.159A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.527A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.656A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.054A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 250 through 256 removed outlier: 3.873A pdb=" N GLN K 255 " --> pdb=" O ILE K 252 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 256 " --> pdb=" O ILE K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 384 Processing helix chain 'K' and resid 728 through 730 No H-bonds generated for 'chain 'K' and resid 728 through 730' Processing helix chain 'K' and resid 755 through 759 Processing helix chain 'K' and resid 985 through 990 Processing helix chain 'K' and resid 1044 through 1062 Processing helix chain 'K' and resid 1069 through 1075 Processing helix chain 'K' and resid 1091 through 1096 Processing helix chain 'K' and resid 1097 through 1100 removed outlier: 3.580A pdb=" N ILE K1100 " --> pdb=" O PHE K1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1097 through 1100' Processing helix chain 'K' and resid 1101 through 1109 Processing helix chain 'K' and resid 1125 through 1138 Processing sheet with id=AA1, first strand: chain 'L' and resid 106 through 107 removed outlier: 3.739A pdb=" N LYS L 106 " --> pdb=" O ILE L 417 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 114 through 119 removed outlier: 4.440A pdb=" N SER L 116 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY L 130 " --> pdb=" O SER L 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 159 through 164 removed outlier: 6.562A pdb=" N SER L 175 " --> pdb=" O THR L 160 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU L 162 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR L 173 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE L 164 " --> pdb=" O GLN L 171 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN L 171 " --> pdb=" O PHE L 164 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP L 185 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE L 190 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 204 through 209 removed outlier: 3.746A pdb=" N SER L 206 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 247 through 250 removed outlier: 3.597A pdb=" N HIS L 247 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA L 249 " --> pdb=" O ALA L 259 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA L 259 " --> pdb=" O ALA L 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 291 through 295 removed outlier: 3.667A pdb=" N ALA L 293 " --> pdb=" O THR L 306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 343 through 344 removed outlier: 5.547A pdb=" N ASP L 376 " --> pdb=" O MET L 382 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET L 382 " --> pdb=" O ASP L 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.966A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.660A pdb=" N THR B 97 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.161A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB4, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.684A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.964A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AB7, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.222A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB9, first strand: chain 'K' and resid 1004 through 1009 removed outlier: 6.736A pdb=" N GLY K1031 " --> pdb=" O ASN K1005 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE K1007 " --> pdb=" O LEU K1029 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU K1029 " --> pdb=" O PHE K1007 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS K1009 " --> pdb=" O SER K1027 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER K1027 " --> pdb=" O HIS K1009 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLY K1026 " --> pdb=" O SER K1042 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER K1042 " --> pdb=" O GLY K1026 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE K1037 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR K 3 " --> pdb=" O LEU K1043 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 17 through 21 removed outlier: 3.533A pdb=" N GLY K 17 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU K 39 " --> pdb=" O GLU K 54 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU K 54 " --> pdb=" O LEU K 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE K 41 " --> pdb=" O VAL K 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 61 through 67 removed outlier: 4.149A pdb=" N ASN K 85 " --> pdb=" O THR K 81 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA K 86 " --> pdb=" O HIS K 105 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS K 105 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE K 88 " --> pdb=" O ARG K 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 121 through 124 Processing sheet with id=AC4, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.609A pdb=" N VAL K 181 " --> pdb=" O ILE K 165 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL K 167 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE K 169 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR K 177 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 164 through 169 removed outlier: 6.609A pdb=" N VAL K 181 " --> pdb=" O ILE K 165 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL K 167 " --> pdb=" O CYS K 179 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE K 169 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N THR K 177 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 218 through 221 Processing sheet with id=AC7, first strand: chain 'K' and resid 258 through 263 removed outlier: 7.061A pdb=" N GLY K 274 " --> pdb=" O VAL K 259 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS K 261 " --> pdb=" O LEU K 272 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU K 272 " --> pdb=" O HIS K 261 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG K 263 " --> pdb=" O ARG K 270 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG K 270 " --> pdb=" O ARG K 263 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU K 280 " --> pdb=" O LEU K 304 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU K 304 " --> pdb=" O LEU K 280 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET K 282 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL K 302 " --> pdb=" O MET K 282 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU K 284 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 300 " --> pdb=" O LEU K 284 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU K 286 " --> pdb=" O LYS K 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 313 through 318 removed outlier: 6.795A pdb=" N VAL K 321 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER K 331 " --> pdb=" O THR K 352 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR K 352 " --> pdb=" O SER K 331 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU K 333 " --> pdb=" O MET K 350 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 359 through 365 removed outlier: 3.746A pdb=" N ASP K 361 " --> pdb=" O CYS K 378 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.038A pdb=" N SER K 738 " --> pdb=" O PRO K 721 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS K 723 " --> pdb=" O LEU K 736 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 720 through 727 removed outlier: 6.038A pdb=" N SER K 738 " --> pdb=" O PRO K 721 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS K 723 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP K 795 " --> pdb=" O VAL K 801 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL K 801 " --> pdb=" O ASP K 795 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER K 762 " --> pdb=" O LEU K 802 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 811 through 821 removed outlier: 5.437A pdb=" N ALA K 813 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA K 834 " --> pdb=" O ALA K 813 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU K 821 " --> pdb=" O ASN K 826 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN K 826 " --> pdb=" O LEU K 821 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR K 827 " --> pdb=" O TYR K 853 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR K 853 " --> pdb=" O THR K 827 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG K 847 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY K 846 " --> pdb=" O GLU K 865 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU K 865 " --> pdb=" O GLY K 846 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE K 848 " --> pdb=" O GLU K 863 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU K 863 " --> pdb=" O ILE K 848 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL K 850 " --> pdb=" O VAL K 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 870 through 876 removed outlier: 3.689A pdb=" N SER K 872 " --> pdb=" O SER K 883 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL K 888 " --> pdb=" O ASN K 904 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN K 904 " --> pdb=" O VAL K 888 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU K 890 " --> pdb=" O GLU K 902 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 911 through 917 removed outlier: 4.934A pdb=" N VAL K 930 " --> pdb=" O ASP K 948 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA K 934 " --> pdb=" O GLU K 944 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU K 944 " --> pdb=" O ALA K 934 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU K 992 " --> pdb=" O ILE K 945 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG K 947 " --> pdb=" O LEU K 992 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU K 994 " --> pdb=" O ARG K 947 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL K 976 " --> pdb=" O VAL K 995 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU K 997 " --> pdb=" O LEU K 974 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU K 974 " --> pdb=" O LEU K 997 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN K 973 " --> pdb=" O GLU K 969 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN K 964 " --> pdb=" O LEU K 960 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 1076 through 1077 Processing sheet with id=AD7, first strand: chain 'K' and resid 1113 through 1114 763 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 332 hydrogen bonds 664 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 11.06 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 18993 1.03 - 1.23: 541 1.23 - 1.43: 9671 1.43 - 1.63: 12225 1.63 - 1.83: 106 Bond restraints: 41536 Sorted by residual: bond pdb=" P 3DR J 94 " pdb=" O5' 3DR J 94 " ideal model delta sigma weight residual 1.720 1.600 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C5' 3DR J 93 " pdb=" H5' 3DR J 93 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C1' 3DR J 93 " pdb="H1'1 3DR J 93 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C3' 3DR J 93 " pdb=" H3' 3DR J 93 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C4' 3DR J 93 " pdb="H4'1 3DR J 93 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.53e+01 ... (remaining 41531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.29: 75161 7.29 - 14.59: 44 14.59 - 21.88: 3 21.88 - 29.17: 14 29.17 - 36.47: 3 Bond angle restraints: 75225 Sorted by residual: angle pdb=" OG1 THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 109.00 72.53 36.47 3.00e+00 1.11e-01 1.48e+02 angle pdb=" CG2 THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 108.00 72.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C SER C 123 " pdb=" CA SER C 123 " pdb=" HA SER C 123 " ideal model delta sigma weight residual 109.00 78.08 30.92 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C GLU C 122 " pdb=" CA GLU C 122 " pdb=" HA GLU C 122 " ideal model delta sigma weight residual 109.00 80.31 28.69 3.00e+00 1.11e-01 9.14e+01 angle pdb=" CA THR B 81 " pdb=" CB THR B 81 " pdb=" HB THR B 81 " ideal model delta sigma weight residual 109.00 80.98 28.02 3.00e+00 1.11e-01 8.72e+01 ... (remaining 75220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 16475 34.94 - 69.89: 1883 69.89 - 104.83: 45 104.83 - 139.78: 9 139.78 - 174.72: 7 Dihedral angle restraints: 18419 sinusoidal: 11908 harmonic: 6511 Sorted by residual: dihedral pdb=" C LYS C 126 " pdb=" N LYS C 126 " pdb=" CA LYS C 126 " pdb=" CB LYS C 126 " ideal model delta harmonic sigma weight residual -122.60 -164.65 42.05 0 2.50e+00 1.60e-01 2.83e+02 dihedral pdb=" N LYS C 126 " pdb=" C LYS C 126 " pdb=" CA LYS C 126 " pdb=" CB LYS C 126 " ideal model delta harmonic sigma weight residual 122.80 164.42 -41.62 0 2.50e+00 1.60e-01 2.77e+02 dihedral pdb=" C SER C 123 " pdb=" N SER C 123 " pdb=" CA SER C 123 " pdb=" CB SER C 123 " ideal model delta harmonic sigma weight residual -122.60 -160.13 37.53 0 2.50e+00 1.60e-01 2.25e+02 ... (remaining 18416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.368: 3568 0.368 - 0.735: 2 0.735 - 1.103: 0 1.103 - 1.470: 1 1.470 - 1.838: 4 Chirality restraints: 3575 Sorted by residual: chirality pdb=" CA LYS C 126 " pdb=" N LYS C 126 " pdb=" C LYS C 126 " pdb=" CB LYS C 126 " both_signs ideal model delta sigma weight residual False 2.51 0.67 1.84 2.00e-01 2.50e+01 8.44e+01 chirality pdb=" CG LEU L 63 " pdb=" CB LEU L 63 " pdb=" CD1 LEU L 63 " pdb=" CD2 LEU L 63 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" CA SER C 123 " pdb=" N SER C 123 " pdb=" C SER C 123 " pdb=" CB SER C 123 " both_signs ideal model delta sigma weight residual False 2.51 0.90 1.61 2.00e-01 2.50e+01 6.50e+01 ... (remaining 3572 not shown) Planarity restraints: 5131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 62 " -0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C PHE F 62 " 0.081 2.00e-02 2.50e+03 pdb=" O PHE F 62 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU F 63 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 65 " -0.023 2.00e-02 2.50e+03 4.65e-02 2.17e+01 pdb=" C ASN B 65 " 0.081 2.00e-02 2.50e+03 pdb=" O ASN B 65 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL B 66 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 65 " 0.023 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C ASN F 65 " -0.080 2.00e-02 2.50e+03 pdb=" O ASN F 65 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL F 66 " 0.027 2.00e-02 2.50e+03 ... (remaining 5128 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1960 2.18 - 2.79: 76436 2.79 - 3.39: 110191 3.39 - 4.00: 153243 4.00 - 4.60: 228400 Nonbonded interactions: 570230 Sorted by model distance: nonbonded pdb=" HZ2 LYS K 383 " pdb=" OE2 GLU K 384 " model vdw 1.577 2.450 nonbonded pdb=" O3' DA J 81 " pdb="HH22 ARG A 41 " model vdw 1.600 2.450 nonbonded pdb=" OG1 THR K 118 " pdb="HH22 ARG K 134 " model vdw 1.628 2.450 nonbonded pdb=" HB THR B 81 " pdb=" HG1 THR B 81 " model vdw 1.638 1.816 nonbonded pdb="HH12 ARG K1057 " pdb=" O ALA K1110 " model vdw 1.638 2.450 ... (remaining 570225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 39 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE or name HH11 or name HH12 or name HH22)) or r \ esid 44 through 136)) } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 22 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name HA \ or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or r \ esid 29 through 103)) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 10 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB or name OG or name H or name HA or name HB2 or name HB3 \ )) or resid 124 through 126)) } ncs_group { reference = chain 'D' selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11)) or resid 33 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3 or name HD2 or name HD3 or name HE )) or resid 88 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 92 or resid 95 through 14 \ 5)) } 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 group one per residue 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: 2.920 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: 0.110 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 44.940 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 22501 Z= 0.716 Angle : 1.190 22.829 31656 Z= 0.870 Chirality : 0.092 1.838 3575 Planarity : 0.007 0.083 3041 Dihedral : 23.891 170.347 9227 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.97 % Favored : 94.67 % Rotamer: Outliers : 0.36 % Allowed : 2.91 % Favored : 96.74 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 1952 helix: 0.47 (0.18), residues: 636 sheet: -0.56 (0.23), residues: 461 loop : -1.61 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG C 43 TYR 0.029 0.005 TYR D 84 PHE 0.038 0.004 PHE K 965 TRP 0.029 0.004 TRP K 953 HIS 0.014 0.003 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.72 (22501) covalent geometry : angle 1.19012 / 0.87 (31656) hydrogen bonds : bond 0.16062 / 17.64 ( 1081) hydrogen bonds : angle 6.01884 / 7.62 ( 2806) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 638 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 632 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.8793 (tt0) cc_final: 0.8569 (tm-30) REVERT: L 214 ARG cc_start: 0.9041 (mtt90) cc_final: 0.8661 (mtp-110) REVERT: L 299 ASP cc_start: 0.9034 (t0) cc_final: 0.8772 (t0) REVERT: L 420 GLN cc_start: 0.9251 (pm20) cc_final: 0.9046 (pm20) REVERT: A 59 THR cc_start: 0.9050 (p) cc_final: 0.8713 (t) REVERT: A 63 ILE cc_start: 0.6968 (mt) cc_final: 0.6734 (mm) REVERT: A 106 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: A 111 CYS cc_start: 0.9488 (m) cc_final: 0.9140 (m) REVERT: A 121 MET cc_start: 0.7839 (mtp) cc_final: 0.7625 (mtt) REVERT: A 125 ILE cc_start: 0.9591 (mt) cc_final: 0.9125 (mm) REVERT: B 27 ILE cc_start: 0.9526 (tp) cc_final: 0.9242 (tp) REVERT: B 28 GLN cc_start: 0.9342 (mm110) cc_final: 0.8921 (mp10) REVERT: C 40 TYR cc_start: 0.8881 (m-80) cc_final: 0.8672 (m-10) REVERT: C 111 ASN cc_start: 0.9092 (p0) cc_final: 0.8879 (p0) REVERT: D 36 GLU cc_start: 0.4108 (pp20) cc_final: 0.3072 (mp0) REVERT: D 68 ASN cc_start: 0.8747 (m110) cc_final: 0.8323 (t0) REVERT: D 72 GLU cc_start: 0.8959 (pt0) cc_final: 0.8736 (pt0) REVERT: D 90 ILE cc_start: 0.8744 (tt) cc_final: 0.8269 (tp) REVERT: D 114 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9152 (mm-30) REVERT: D 121 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9115 (tppt) REVERT: E 63 ILE cc_start: 0.8760 (mt) cc_final: 0.8128 (mt) REVERT: E 75 ILE cc_start: 0.9516 (mt) cc_final: 0.9286 (tp) REVERT: E 79 PHE cc_start: 0.8836 (m-80) cc_final: 0.8298 (m-10) REVERT: E 94 GLN cc_start: 0.9600 (tt0) cc_final: 0.8151 (tp40) REVERT: E 98 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8725 (mt-10) REVERT: E 106 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: E 113 ILE cc_start: 0.9458 (mt) cc_final: 0.9242 (mt) REVERT: E 123 LYS cc_start: 0.9337 (pttt) cc_final: 0.8972 (pttm) REVERT: F 50 LEU cc_start: 0.9378 (mt) cc_final: 0.9134 (mp) REVERT: F 54 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8903 (mm-30) REVERT: F 65 ASN cc_start: 0.9492 (m-40) cc_final: 0.9281 (m-40) REVERT: F 75 GLU cc_start: 0.9488 (tt0) cc_final: 0.8867 (tp30) REVERT: F 97 THR cc_start: 0.9132 (m) cc_final: 0.8499 (p) REVERT: G 18 ARG cc_start: 0.8392 (mtm180) cc_final: 0.8122 (mtp180) REVERT: G 21 ARG cc_start: 0.8871 (mtp180) cc_final: 0.8565 (mtm-85) REVERT: G 37 LYS cc_start: 0.9436 (mttm) cc_final: 0.8845 (tmtt) REVERT: G 57 GLU cc_start: 0.8121 (tt0) cc_final: 0.7570 (tt0) REVERT: G 60 THR cc_start: 0.9456 (m) cc_final: 0.9255 (p) REVERT: G 101 VAL cc_start: 0.8429 (t) cc_final: 0.8125 (t) REVERT: G 103 ILE cc_start: 0.9495 (mm) cc_final: 0.8980 (tp) REVERT: H 93 ARG cc_start: 0.9322 (mtp-110) cc_final: 0.8931 (tmm-80) REVERT: H 97 THR cc_start: 0.9712 (m) cc_final: 0.9403 (p) REVERT: H 114 GLU cc_start: 0.9283 (mm-30) cc_final: 0.9010 (mm-30) REVERT: K 15 VAL cc_start: 0.7997 (t) cc_final: 0.7744 (p) REVERT: K 930 VAL cc_start: 0.7463 (m) cc_final: 0.6826 (m) REVERT: K 976 VAL cc_start: 0.9705 (t) cc_final: 0.9385 (p) REVERT: K 1070 HIS cc_start: 0.9058 (t-90) cc_final: 0.8357 (t70) REVERT: K 1120 MET cc_start: 0.8578 (mmp) cc_final: 0.7569 (tmm) REVERT: K 1127 ASP cc_start: 0.8861 (m-30) cc_final: 0.8608 (p0) outliers start: 6 outliers final: 3 residues processed: 636 average time/residue: 0.4198 time to fit residues: 377.2111 Evaluate side-chains 483 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 478 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 91 GLN ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 385 GLN L 398 ASN C 105 GLN D 68 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 64 ASN K 93 GLN ** K 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.069108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049673 restraints weight = 257439.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053688 restraints weight = 109556.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056287 restraints weight = 58497.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057966 restraints weight = 36183.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059053 restraints weight = 25283.911| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 22501 Z= 0.223 Angle : 0.765 12.425 31656 Z= 0.456 Chirality : 0.061 1.772 3575 Planarity : 0.006 0.077 3041 Dihedral : 27.869 178.536 5424 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 0.06 % Allowed : 2.31 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.62 (0.18), residues: 1952 helix: 1.29 (0.20), residues: 651 sheet: -0.76 (0.23), residues: 465 loop : -1.57 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 753 TYR 0.021 0.002 TYR H 41 PHE 0.017 0.002 PHE K 78 TRP 0.021 0.002 TRP L 83 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.22 (22501) covalent geometry : angle 0.76517 / 0.46 (31656) hydrogen bonds : bond 0.07280 / 8.05 ( 1081) hydrogen bonds : angle 5.16027 / 6.53 ( 2806) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.8979 (tt0) cc_final: 0.8668 (tm-30) REVERT: L 292 ASN cc_start: 0.8940 (m-40) cc_final: 0.8650 (m110) REVERT: L 299 ASP cc_start: 0.8824 (t0) cc_final: 0.8464 (t0) REVERT: L 348 TYR cc_start: 0.8023 (m-80) cc_final: 0.7725 (m-80) REVERT: L 350 LEU cc_start: 0.7791 (mt) cc_final: 0.7369 (mm) REVERT: A 63 ILE cc_start: 0.6869 (mt) cc_final: 0.6479 (mm) REVERT: A 91 MET cc_start: 0.9406 (mtp) cc_final: 0.9182 (mtp) REVERT: A 106 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8869 (tm-30) REVERT: A 111 CYS cc_start: 0.9462 (m) cc_final: 0.9019 (t) REVERT: C 40 TYR cc_start: 0.8695 (m-80) cc_final: 0.8355 (m-80) REVERT: C 74 ASN cc_start: 0.9616 (t0) cc_final: 0.9341 (t0) REVERT: C 88 ILE cc_start: 0.8681 (mt) cc_final: 0.8144 (tp) REVERT: C 96 LYS cc_start: 0.9526 (tmtt) cc_final: 0.9216 (tptp) REVERT: D 68 ASN cc_start: 0.8631 (m-40) cc_final: 0.8224 (t0) REVERT: D 80 ARG cc_start: 0.8940 (mtp85) cc_final: 0.8239 (mtp85) REVERT: D 90 ILE cc_start: 0.8780 (tt) cc_final: 0.8152 (tp) REVERT: D 94 GLU cc_start: 0.9488 (mp0) cc_final: 0.9088 (mp0) REVERT: D 114 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9193 (mm-30) REVERT: D 121 LYS cc_start: 0.9523 (mtpt) cc_final: 0.9071 (tppt) REVERT: E 61 LEU cc_start: 0.8838 (mp) cc_final: 0.6691 (mp) REVERT: E 75 ILE cc_start: 0.9630 (mt) cc_final: 0.9346 (tp) REVERT: E 79 PHE cc_start: 0.8670 (m-80) cc_final: 0.8064 (m-10) REVERT: E 91 MET cc_start: 0.9304 (mmm) cc_final: 0.8879 (mmm) REVERT: E 94 GLN cc_start: 0.9527 (tt0) cc_final: 0.8594 (tt0) REVERT: E 95 GLU cc_start: 0.9413 (mm-30) cc_final: 0.8947 (mm-30) REVERT: E 98 GLU cc_start: 0.9376 (mt-10) cc_final: 0.8976 (mt-10) REVERT: E 123 LYS cc_start: 0.9343 (pttt) cc_final: 0.8950 (ptpp) REVERT: E 134 GLU cc_start: 0.7017 (tp30) cc_final: 0.6451 (tp30) REVERT: F 54 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8798 (mm-30) REVERT: F 75 GLU cc_start: 0.9566 (tt0) cc_final: 0.8980 (tp30) REVERT: F 97 THR cc_start: 0.9066 (m) cc_final: 0.8533 (p) REVERT: G 18 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7784 (mtt180) REVERT: G 37 LYS cc_start: 0.9424 (mttm) cc_final: 0.9158 (tppt) REVERT: G 103 ILE cc_start: 0.9293 (mm) cc_final: 0.8765 (tp) REVERT: H 114 GLU cc_start: 0.9269 (mm-30) cc_final: 0.9023 (mm-30) REVERT: K 112 ILE cc_start: 0.6531 (pt) cc_final: 0.6223 (pt) REVERT: K 300 LEU cc_start: 0.9347 (mt) cc_final: 0.9070 (mt) REVERT: K 360 VAL cc_start: 0.7385 (m) cc_final: 0.7121 (m) REVERT: K 927 MET cc_start: 0.7081 (ptm) cc_final: 0.6802 (ppp) REVERT: K 1070 HIS cc_start: 0.9117 (t-90) cc_final: 0.8177 (t70) REVERT: K 1120 MET cc_start: 0.9024 (mmp) cc_final: 0.8114 (tmm) REVERT: K 1127 ASP cc_start: 0.8917 (m-30) cc_final: 0.8641 (p0) outliers start: 1 outliers final: 0 residues processed: 529 average time/residue: 0.3873 time to fit residues: 298.3546 Evaluate side-chains 458 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [9, 40, 135, 140, 172, 83, 70, 165, 56, 14, 173] chunk 9 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 140 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 173 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN C 113 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 907 ASN K1034 ASN K1055 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047893 restraints weight = 256961.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051740 restraints weight = 109378.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054257 restraints weight = 58379.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055883 restraints weight = 35987.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056934 restraints weight = 24978.364| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 22501 Z= 0.260 Angle : 0.753 12.190 31656 Z= 0.451 Chirality : 0.060 1.720 3575 Planarity : 0.006 0.123 3041 Dihedral : 27.924 178.670 5424 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 1952 helix: 0.83 (0.19), residues: 655 sheet: -0.86 (0.23), residues: 454 loop : -1.67 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 753 TYR 0.020 0.002 TYR K 853 PHE 0.019 0.002 PHE K 965 TRP 0.037 0.003 TRP K1073 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.26 (22501) covalent geometry : angle 0.75300 / 0.45 (31656) hydrogen bonds : bond 0.07238 / 7.93 ( 1081) hydrogen bonds : angle 5.33053 / 6.68 ( 2806) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 509 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 GLN cc_start: 0.9069 (tt0) cc_final: 0.8628 (tm-30) REVERT: L 292 ASN cc_start: 0.8910 (m-40) cc_final: 0.8654 (m110) REVERT: L 299 ASP cc_start: 0.8896 (t0) cc_final: 0.8555 (t0) REVERT: L 348 TYR cc_start: 0.8234 (m-80) cc_final: 0.7853 (m-80) REVERT: L 350 LEU cc_start: 0.7798 (mt) cc_final: 0.7301 (mm) REVERT: A 57 LYS cc_start: 0.9563 (ttpt) cc_final: 0.9273 (tppt) REVERT: A 63 ILE cc_start: 0.7071 (mt) cc_final: 0.6693 (mm) REVERT: A 106 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8929 (tm-30) REVERT: A 111 CYS cc_start: 0.9500 (m) cc_final: 0.9103 (t) REVERT: A 121 MET cc_start: 0.5054 (mtt) cc_final: 0.4553 (mtt) REVERT: C 40 TYR cc_start: 0.8922 (m-80) cc_final: 0.8536 (m-80) REVERT: C 74 ASN cc_start: 0.9546 (t0) cc_final: 0.9334 (t0) REVERT: C 88 ILE cc_start: 0.8800 (mt) cc_final: 0.8330 (tp) REVERT: C 103 ILE cc_start: 0.9273 (mm) cc_final: 0.8919 (tp) REVERT: D 68 ASN cc_start: 0.8603 (m-40) cc_final: 0.8277 (t0) REVERT: D 80 ARG cc_start: 0.9203 (mtp85) cc_final: 0.8219 (mtp85) REVERT: D 90 ILE cc_start: 0.8927 (tt) cc_final: 0.8457 (tp) REVERT: D 94 GLU cc_start: 0.9398 (mp0) cc_final: 0.9147 (mp0) REVERT: D 114 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9225 (mm-30) REVERT: D 121 LYS cc_start: 0.9527 (mtpt) cc_final: 0.9101 (tppt) REVERT: E 61 LEU cc_start: 0.8895 (mp) cc_final: 0.8043 (mp) REVERT: E 94 GLN cc_start: 0.9521 (tt0) cc_final: 0.8757 (tt0) REVERT: E 98 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9057 (mt-10) REVERT: E 123 LYS cc_start: 0.9375 (pttt) cc_final: 0.9109 (pttt) REVERT: E 134 GLU cc_start: 0.7069 (tp30) cc_final: 0.6463 (tp30) REVERT: F 54 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8807 (mm-30) REVERT: F 65 ASN cc_start: 0.9326 (m110) cc_final: 0.9000 (m110) REVERT: F 75 GLU cc_start: 0.9572 (tt0) cc_final: 0.8974 (tp30) REVERT: G 18 ARG cc_start: 0.8227 (mtm180) cc_final: 0.7857 (mtt180) REVERT: G 37 LYS cc_start: 0.9364 (mttm) cc_final: 0.9145 (tptp) REVERT: G 40 TYR cc_start: 0.8763 (m-80) cc_final: 0.8384 (m-80) REVERT: G 103 ILE cc_start: 0.9282 (mm) cc_final: 0.8754 (tp) REVERT: H 114 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8974 (mm-30) REVERT: H 117 LYS cc_start: 0.9767 (ttpt) cc_final: 0.9409 (tmtt) REVERT: K 84 TYR cc_start: 0.8929 (m-80) cc_final: 0.8632 (m-80) REVERT: K 112 ILE cc_start: 0.6910 (pt) cc_final: 0.6610 (pt) REVERT: K 130 MET cc_start: 0.7874 (ptp) cc_final: 0.7671 (pmm) REVERT: K 300 LEU cc_start: 0.9370 (mt) cc_final: 0.9090 (mt) REVERT: K 927 MET cc_start: 0.7180 (ptm) cc_final: 0.6836 (ppp) REVERT: K 1070 HIS cc_start: 0.9227 (t-90) cc_final: 0.8145 (t70) REVERT: K 1120 MET cc_start: 0.9061 (mmp) cc_final: 0.8160 (ppp) REVERT: K 1127 ASP cc_start: 0.8886 (m-30) cc_final: 0.8625 (p0) outliers start: 1 outliers final: 0 residues processed: 508 average time/residue: 0.3814 time to fit residues: 282.8362 Evaluate side-chains 445 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [92, 100, 23, 52, 11, 159, 185, 216, 163, 33, 77] chunk 92 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 87 GLN L 170 ASN ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 65 ASN G 39 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 845 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.043719 restraints weight = 277236.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047189 restraints weight = 118663.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049454 restraints weight = 63769.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.050926 restraints weight = 39715.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.051888 restraints weight = 27850.948| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.176 22501 Z= 0.352 Angle : 0.834 12.219 31656 Z= 0.494 Chirality : 0.060 1.659 3575 Planarity : 0.007 0.172 3041 Dihedral : 28.125 178.526 5424 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.76 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.17), residues: 1952 helix: -0.61 (0.18), residues: 655 sheet: -1.17 (0.24), residues: 424 loop : -1.89 (0.18), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 100 TYR 0.028 0.003 TYR K 853 PHE 0.032 0.003 PHE F 101 TRP 0.017 0.003 TRP K1073 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.35 (22501) covalent geometry : angle 0.83428 / 0.49 (31656) hydrogen bonds : bond 0.08828 / 9.56 ( 1081) hydrogen bonds : angle 6.01059 / 7.55 ( 2806) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 292 ASN cc_start: 0.8985 (m-40) cc_final: 0.8747 (m-40) REVERT: L 299 ASP cc_start: 0.9066 (t0) cc_final: 0.8771 (t0) REVERT: A 57 LYS cc_start: 0.9591 (ttpt) cc_final: 0.9308 (tppt) REVERT: A 63 ILE cc_start: 0.7211 (mt) cc_final: 0.6786 (mm) REVERT: A 106 GLU cc_start: 0.9234 (tm-30) cc_final: 0.9005 (tm-30) REVERT: A 124 ASP cc_start: 0.9114 (m-30) cc_final: 0.8517 (m-30) REVERT: C 40 TYR cc_start: 0.9014 (m-80) cc_final: 0.8803 (m-10) REVERT: C 74 ASN cc_start: 0.9565 (t0) cc_final: 0.9361 (t0) REVERT: C 88 ILE cc_start: 0.8981 (mt) cc_final: 0.8541 (tp) REVERT: C 103 ILE cc_start: 0.9356 (mm) cc_final: 0.9021 (tp) REVERT: D 36 GLU cc_start: 0.5030 (pp20) cc_final: 0.2375 (mm-30) REVERT: D 68 ASN cc_start: 0.8951 (m-40) cc_final: 0.8346 (t0) REVERT: D 72 GLU cc_start: 0.8655 (pt0) cc_final: 0.8360 (pt0) REVERT: D 90 ILE cc_start: 0.9277 (tt) cc_final: 0.8993 (tp) REVERT: D 93 ARG cc_start: 0.9542 (ttm170) cc_final: 0.9232 (ttm-80) REVERT: D 94 GLU cc_start: 0.9532 (mp0) cc_final: 0.9173 (mp0) REVERT: D 114 GLU cc_start: 0.9562 (mm-30) cc_final: 0.9227 (mm-30) REVERT: D 121 LYS cc_start: 0.9556 (mtpt) cc_final: 0.9159 (tppt) REVERT: E 56 GLN cc_start: 0.9278 (mt0) cc_final: 0.8890 (mt0) REVERT: E 74 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8882 (pt0) REVERT: E 98 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9229 (mt-10) REVERT: E 123 LYS cc_start: 0.9349 (pttt) cc_final: 0.9048 (ptpp) REVERT: E 125 ILE cc_start: 0.9640 (mt) cc_final: 0.9428 (mm) REVERT: E 134 GLU cc_start: 0.6990 (tp30) cc_final: 0.6591 (tp30) REVERT: F 54 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8903 (mm-30) REVERT: F 65 ASN cc_start: 0.9433 (m-40) cc_final: 0.9110 (m110) REVERT: F 75 GLU cc_start: 0.9541 (tt0) cc_final: 0.8931 (tp30) REVERT: G 40 TYR cc_start: 0.8761 (m-80) cc_final: 0.8417 (m-80) REVERT: G 103 ILE cc_start: 0.9343 (mm) cc_final: 0.8814 (tp) REVERT: H 58 LYS cc_start: 0.9206 (mtpt) cc_final: 0.8880 (mmmm) REVERT: H 114 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9249 (mm-30) REVERT: H 117 LYS cc_start: 0.9787 (ttpt) cc_final: 0.9438 (tmtt) REVERT: K 84 TYR cc_start: 0.8970 (m-80) cc_final: 0.8698 (m-80) REVERT: K 112 ILE cc_start: 0.7657 (pt) cc_final: 0.7413 (pt) REVERT: K 130 MET cc_start: 0.7960 (ptp) cc_final: 0.7724 (pmm) REVERT: K 131 ILE cc_start: 0.9424 (mt) cc_final: 0.9201 (mm) REVERT: K 300 LEU cc_start: 0.9374 (mt) cc_final: 0.9126 (mt) REVERT: K 927 MET cc_start: 0.7613 (ptm) cc_final: 0.7302 (ppp) REVERT: K 1070 HIS cc_start: 0.9183 (t-90) cc_final: 0.8334 (t70) REVERT: K 1120 MET cc_start: 0.9078 (mmp) cc_final: 0.8236 (tmm) REVERT: K 1127 ASP cc_start: 0.8909 (m-30) cc_final: 0.8648 (p0) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.3832 time to fit residues: 269.5660 Evaluate side-chains 425 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [56, 28, 71, 164, 43, 99, 155, 127, 97, 66, 126] chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 155 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 398 ASN ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.066463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047520 restraints weight = 262267.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.051349 restraints weight = 112909.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053825 restraints weight = 60746.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055432 restraints weight = 38002.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056448 restraints weight = 26823.958| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 22501 Z= 0.162 Angle : 0.694 12.091 31656 Z= 0.414 Chirality : 0.060 1.672 3575 Planarity : 0.005 0.063 3041 Dihedral : 28.179 176.580 5424 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 0.06 % Allowed : 1.13 % Favored : 98.81 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.18), residues: 1952 helix: 0.57 (0.19), residues: 660 sheet: -1.07 (0.25), residues: 415 loop : -1.77 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 64 TYR 0.017 0.002 TYR E 100 PHE 0.069 0.002 PHE E 68 TRP 0.010 0.002 TRP L 320 HIS 0.007 0.001 HIS E 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (22501) covalent geometry : angle 0.69356 / 0.41 (31656) hydrogen bonds : bond 0.06216 / 6.70 ( 1081) hydrogen bonds : angle 5.05559 / 6.42 ( 2806) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 489 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 292 ASN cc_start: 0.8906 (m-40) cc_final: 0.8647 (m110) REVERT: L 299 ASP cc_start: 0.8961 (t0) cc_final: 0.8656 (t0) REVERT: A 57 LYS cc_start: 0.9529 (ttpt) cc_final: 0.9239 (tppt) REVERT: A 106 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8870 (tm-30) REVERT: B 65 ASN cc_start: 0.9498 (m110) cc_final: 0.9238 (m110) REVERT: C 40 TYR cc_start: 0.8825 (m-80) cc_final: 0.8616 (m-10) REVERT: C 42 GLU cc_start: 0.9091 (mp0) cc_final: 0.8635 (mp0) REVERT: C 74 ASN cc_start: 0.9545 (t0) cc_final: 0.9331 (t0) REVERT: C 103 ILE cc_start: 0.9259 (mm) cc_final: 0.8931 (tp) REVERT: D 36 GLU cc_start: 0.5257 (pp20) cc_final: 0.3391 (mm-30) REVERT: D 68 ASN cc_start: 0.8831 (m-40) cc_final: 0.8216 (t0) REVERT: D 72 GLU cc_start: 0.8615 (pt0) cc_final: 0.8286 (pt0) REVERT: D 94 GLU cc_start: 0.9456 (mp0) cc_final: 0.9220 (mp0) REVERT: D 121 LYS cc_start: 0.9510 (mtpt) cc_final: 0.9067 (tppt) REVERT: E 74 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8724 (pt0) REVERT: E 77 GLN cc_start: 0.8825 (tp40) cc_final: 0.8586 (mm110) REVERT: E 97 CYS cc_start: 0.9379 (m) cc_final: 0.8904 (t) REVERT: E 98 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9012 (mt-10) REVERT: E 101 LEU cc_start: 0.9641 (mt) cc_final: 0.9366 (mt) REVERT: E 123 LYS cc_start: 0.9250 (pttt) cc_final: 0.8959 (pttt) REVERT: E 134 GLU cc_start: 0.6902 (tp30) cc_final: 0.6259 (tp30) REVERT: F 54 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8763 (mm-30) REVERT: F 63 LEU cc_start: 0.9792 (mt) cc_final: 0.9577 (mt) REVERT: F 65 ASN cc_start: 0.9363 (m-40) cc_final: 0.9022 (m110) REVERT: G 103 ILE cc_start: 0.9311 (mm) cc_final: 0.8733 (tp) REVERT: H 58 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8802 (mmmm) REVERT: H 114 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9220 (mm-30) REVERT: H 117 LYS cc_start: 0.9769 (ttpt) cc_final: 0.9436 (tmtt) REVERT: K 84 TYR cc_start: 0.8915 (m-80) cc_final: 0.8600 (m-80) REVERT: K 130 MET cc_start: 0.7842 (ptp) cc_final: 0.7561 (pmm) REVERT: K 300 LEU cc_start: 0.9342 (mt) cc_final: 0.9086 (mt) REVERT: K 927 MET cc_start: 0.7568 (ptm) cc_final: 0.7299 (ppp) REVERT: K 1070 HIS cc_start: 0.9118 (t-90) cc_final: 0.8391 (t70) REVERT: K 1120 MET cc_start: 0.9067 (mmp) cc_final: 0.8230 (tmm) REVERT: K 1127 ASP cc_start: 0.8858 (m-30) cc_final: 0.8609 (p0) outliers start: 1 outliers final: 0 residues processed: 488 average time/residue: 0.3805 time to fit residues: 272.4267 Evaluate side-chains 427 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [92, 18, 51, 85, 218, 34, 107, 22, 121, 63, 184] chunk 92 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN A 69 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045187 restraints weight = 270447.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048770 restraints weight = 115190.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.051128 restraints weight = 61899.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052657 restraints weight = 38650.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053663 restraints weight = 27223.563| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22501 Z= 0.244 Angle : 0.716 12.169 31656 Z= 0.428 Chirality : 0.059 1.687 3575 Planarity : 0.005 0.068 3041 Dihedral : 28.168 178.819 5424 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.71 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.18), residues: 1952 helix: 0.34 (0.19), residues: 661 sheet: -1.10 (0.26), residues: 407 loop : -1.79 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 41 TYR 0.019 0.002 TYR K 853 PHE 0.020 0.002 PHE K 965 TRP 0.011 0.002 TRP L 270 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.24 (22501) covalent geometry : angle 0.71606 / 0.43 (31656) hydrogen bonds : bond 0.06637 / 7.24 ( 1081) hydrogen bonds : angle 5.35285 / 6.81 ( 2806) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 471 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 299 ASP cc_start: 0.9016 (t0) cc_final: 0.8730 (t0) REVERT: A 57 LYS cc_start: 0.9558 (ttpt) cc_final: 0.9270 (tppt) REVERT: A 91 MET cc_start: 0.9598 (mtp) cc_final: 0.9386 (mtp) REVERT: A 106 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8925 (tm-30) REVERT: B 65 ASN cc_start: 0.9489 (m110) cc_final: 0.9284 (m110) REVERT: C 74 ASN cc_start: 0.9576 (t0) cc_final: 0.9366 (t0) REVERT: D 36 GLU cc_start: 0.5402 (pp20) cc_final: 0.3411 (mm-30) REVERT: D 68 ASN cc_start: 0.8871 (m-40) cc_final: 0.8255 (t0) REVERT: D 72 GLU cc_start: 0.8698 (pt0) cc_final: 0.8347 (pt0) REVERT: D 90 ILE cc_start: 0.9229 (tt) cc_final: 0.8901 (tp) REVERT: D 93 ARG cc_start: 0.9531 (ttm170) cc_final: 0.9303 (ttm-80) REVERT: D 94 GLU cc_start: 0.9567 (mp0) cc_final: 0.9176 (mp0) REVERT: D 114 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9132 (mm-30) REVERT: D 121 LYS cc_start: 0.9560 (mtpt) cc_final: 0.9148 (tppt) REVERT: E 71 LEU cc_start: 0.9635 (tp) cc_final: 0.9308 (mm) REVERT: E 79 PHE cc_start: 0.9155 (m-80) cc_final: 0.8706 (m-80) REVERT: E 98 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9177 (mt-10) REVERT: E 123 LYS cc_start: 0.9373 (pttt) cc_final: 0.8989 (pttm) REVERT: E 134 GLU cc_start: 0.7083 (tp30) cc_final: 0.6406 (tp30) REVERT: F 54 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8827 (mm-30) REVERT: F 65 ASN cc_start: 0.9424 (m-40) cc_final: 0.9110 (m110) REVERT: F 75 GLU cc_start: 0.9506 (tt0) cc_final: 0.8851 (tp30) REVERT: G 37 LYS cc_start: 0.9332 (tptp) cc_final: 0.9039 (tptp) REVERT: G 40 TYR cc_start: 0.8702 (m-80) cc_final: 0.8359 (m-80) REVERT: G 42 GLU cc_start: 0.9040 (mp0) cc_final: 0.8837 (mp0) REVERT: G 103 ILE cc_start: 0.9323 (mm) cc_final: 0.8775 (tp) REVERT: G 116 LEU cc_start: 0.9157 (mt) cc_final: 0.8839 (pp) REVERT: H 58 LYS cc_start: 0.9195 (mtpt) cc_final: 0.8861 (mmmm) REVERT: H 114 GLU cc_start: 0.9580 (mm-30) cc_final: 0.9266 (mm-30) REVERT: H 117 LYS cc_start: 0.9815 (ttpt) cc_final: 0.9457 (tmtt) REVERT: K 84 TYR cc_start: 0.8951 (m-80) cc_final: 0.8677 (m-80) REVERT: K 130 MET cc_start: 0.7952 (ptp) cc_final: 0.7626 (pmm) REVERT: K 300 LEU cc_start: 0.9322 (mt) cc_final: 0.9066 (mt) REVERT: K 927 MET cc_start: 0.7659 (ptm) cc_final: 0.7427 (ppp) REVERT: K 1070 HIS cc_start: 0.9169 (t-90) cc_final: 0.8443 (t70) REVERT: K 1120 MET cc_start: 0.9059 (mmp) cc_final: 0.8221 (tmm) REVERT: K 1127 ASP cc_start: 0.8839 (m-30) cc_final: 0.8590 (p0) outliers start: 1 outliers final: 0 residues processed: 470 average time/residue: 0.3745 time to fit residues: 259.1686 Evaluate side-chains 425 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [204, 45, 103, 149, 14, 194, 18, 64, 150, 168, 79] chunk 204 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 184 GLN ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 GLN K 990 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.042801 restraints weight = 281522.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046161 restraints weight = 120742.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048374 restraints weight = 65181.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049805 restraints weight = 40765.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050762 restraints weight = 28845.664| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.174 22501 Z= 0.328 Angle : 0.800 12.181 31656 Z= 0.474 Chirality : 0.060 1.656 3575 Planarity : 0.007 0.147 3041 Dihedral : 28.334 178.146 5424 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.50 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 1952 helix: -0.55 (0.18), residues: 657 sheet: -1.26 (0.26), residues: 409 loop : -1.96 (0.18), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 41 TYR 0.054 0.003 TYR F 52 PHE 0.052 0.003 PHE L 172 TRP 0.024 0.003 TRP L 119 HIS 0.015 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.33 (22501) covalent geometry : angle 0.79977 / 0.47 (31656) hydrogen bonds : bond 0.08322 / 9.04 ( 1081) hydrogen bonds : angle 5.92953 / 7.56 ( 2806) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 255 ASP cc_start: 0.8864 (p0) cc_final: 0.6692 (p0) REVERT: L 299 ASP cc_start: 0.9101 (t0) cc_final: 0.8822 (t0) REVERT: A 57 LYS cc_start: 0.9565 (ttpt) cc_final: 0.9275 (tppt) REVERT: A 124 ASP cc_start: 0.8844 (m-30) cc_final: 0.8594 (m-30) REVERT: B 65 ASN cc_start: 0.9493 (m110) cc_final: 0.9213 (m110) REVERT: D 36 GLU cc_start: 0.5486 (pp20) cc_final: 0.3573 (mm-30) REVERT: D 68 ASN cc_start: 0.9005 (m-40) cc_final: 0.8396 (t0) REVERT: D 72 GLU cc_start: 0.8763 (pt0) cc_final: 0.8338 (pt0) REVERT: D 90 ILE cc_start: 0.9395 (tt) cc_final: 0.9102 (tp) REVERT: D 93 ARG cc_start: 0.9549 (ttm170) cc_final: 0.9302 (ttm-80) REVERT: D 94 GLU cc_start: 0.9552 (mp0) cc_final: 0.9205 (mp0) REVERT: D 96 GLN cc_start: 0.9575 (tt0) cc_final: 0.9014 (tm-30) REVERT: E 71 LEU cc_start: 0.9647 (tp) cc_final: 0.9325 (mm) REVERT: E 79 PHE cc_start: 0.9284 (m-80) cc_final: 0.8849 (m-80) REVERT: E 98 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9221 (mt-10) REVERT: E 134 GLU cc_start: 0.7205 (tp30) cc_final: 0.6553 (tp30) REVERT: F 54 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8803 (mm-30) REVERT: F 65 ASN cc_start: 0.9452 (m-40) cc_final: 0.9162 (m-40) REVERT: G 40 TYR cc_start: 0.8814 (m-80) cc_final: 0.8516 (m-80) REVERT: G 42 GLU cc_start: 0.9020 (mp0) cc_final: 0.8817 (mp0) REVERT: G 103 ILE cc_start: 0.9374 (mm) cc_final: 0.8827 (tp) REVERT: G 116 LEU cc_start: 0.9239 (mt) cc_final: 0.8940 (pp) REVERT: H 58 LYS cc_start: 0.9277 (mtpt) cc_final: 0.8961 (mmmm) REVERT: H 114 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9387 (mm-30) REVERT: H 117 LYS cc_start: 0.9822 (ttpt) cc_final: 0.9499 (tmtt) REVERT: K 130 MET cc_start: 0.8027 (ptp) cc_final: 0.7680 (pmm) REVERT: K 146 ASP cc_start: 0.8566 (t70) cc_final: 0.8365 (t70) REVERT: K 300 LEU cc_start: 0.9338 (mt) cc_final: 0.9113 (mt) REVERT: K 835 MET cc_start: 0.8633 (mmp) cc_final: 0.8397 (mmm) REVERT: K 1070 HIS cc_start: 0.9185 (t-90) cc_final: 0.8452 (t70) REVERT: K 1120 MET cc_start: 0.9052 (mmp) cc_final: 0.8229 (tmm) REVERT: K 1127 ASP cc_start: 0.8881 (m-30) cc_final: 0.8631 (p0) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3727 time to fit residues: 254.6986 Evaluate side-chains 411 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [64, 166, 121, 207, 163, 204, 114, 40, 74, 203, 65] chunk 64 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN H 96 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045337 restraints weight = 269050.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048906 restraints weight = 116818.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051247 restraints weight = 63369.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.052773 restraints weight = 39885.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053765 restraints weight = 28343.741| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22501 Z= 0.171 Angle : 0.682 11.834 31656 Z= 0.408 Chirality : 0.059 1.657 3575 Planarity : 0.005 0.077 3041 Dihedral : 28.395 178.069 5424 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer: Outliers : 0.06 % Allowed : 0.71 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 1952 helix: 0.36 (0.19), residues: 662 sheet: -1.25 (0.25), residues: 420 loop : -1.75 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 37 TYR 0.022 0.002 TYR H 84 PHE 0.020 0.002 PHE K 965 TRP 0.010 0.002 TRP L 320 HIS 0.007 0.001 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (22501) covalent geometry : angle 0.68223 / 0.41 (31656) hydrogen bonds : bond 0.06122 / 6.64 ( 1081) hydrogen bonds : angle 5.17310 / 6.65 ( 2806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 472 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 250 LEU cc_start: 0.7890 (mm) cc_final: 0.7667 (mm) REVERT: L 299 ASP cc_start: 0.9076 (t0) cc_final: 0.8797 (t0) REVERT: A 57 LYS cc_start: 0.9534 (ttpt) cc_final: 0.9202 (tppt) REVERT: A 91 MET cc_start: 0.9645 (mtp) cc_final: 0.9421 (mtp) REVERT: A 106 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8925 (tm-30) REVERT: C 42 GLU cc_start: 0.8972 (mp0) cc_final: 0.8674 (mp0) REVERT: C 74 ASN cc_start: 0.9565 (t0) cc_final: 0.9363 (t0) REVERT: D 35 LYS cc_start: 0.8678 (mppt) cc_final: 0.8478 (mmtm) REVERT: D 36 GLU cc_start: 0.5659 (pp20) cc_final: 0.3378 (mm-30) REVERT: D 68 ASN cc_start: 0.8937 (m-40) cc_final: 0.8260 (t0) REVERT: D 72 GLU cc_start: 0.8735 (pt0) cc_final: 0.8271 (pt0) REVERT: D 90 ILE cc_start: 0.9324 (tt) cc_final: 0.8980 (tp) REVERT: D 93 ARG cc_start: 0.9527 (ttm170) cc_final: 0.9299 (ttm-80) REVERT: D 94 GLU cc_start: 0.9546 (mp0) cc_final: 0.9200 (mp0) REVERT: D 96 GLN cc_start: 0.9538 (tt0) cc_final: 0.8976 (tm-30) REVERT: D 114 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9135 (mm-30) REVERT: D 121 LYS cc_start: 0.9564 (mtpt) cc_final: 0.9126 (tppt) REVERT: E 71 LEU cc_start: 0.9616 (tp) cc_final: 0.9301 (mm) REVERT: E 79 PHE cc_start: 0.9222 (m-80) cc_final: 0.8807 (m-80) REVERT: E 94 GLN cc_start: 0.9426 (tt0) cc_final: 0.8140 (tp40) REVERT: E 98 GLU cc_start: 0.9413 (mt-10) cc_final: 0.8305 (mt-10) REVERT: E 119 THR cc_start: 0.9000 (m) cc_final: 0.8429 (m) REVERT: E 121 MET cc_start: 0.8551 (mtp) cc_final: 0.8108 (mtp) REVERT: E 124 ASP cc_start: 0.9400 (m-30) cc_final: 0.9089 (m-30) REVERT: E 134 GLU cc_start: 0.7183 (tp30) cc_final: 0.6524 (tp30) REVERT: F 54 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8729 (mm-30) REVERT: F 65 ASN cc_start: 0.9398 (m-40) cc_final: 0.9081 (m110) REVERT: G 37 LYS cc_start: 0.9389 (tptp) cc_final: 0.9106 (tptp) REVERT: G 40 TYR cc_start: 0.8655 (m-80) cc_final: 0.8368 (m-80) REVERT: G 42 GLU cc_start: 0.8980 (mp0) cc_final: 0.8749 (mp0) REVERT: G 103 ILE cc_start: 0.9342 (mm) cc_final: 0.8799 (tp) REVERT: H 58 LYS cc_start: 0.9231 (mtpt) cc_final: 0.8899 (mmmm) REVERT: H 114 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9284 (mm-30) REVERT: H 117 LYS cc_start: 0.9814 (ttpt) cc_final: 0.9476 (tmtt) REVERT: K 60 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8786 (tptt) REVERT: K 130 MET cc_start: 0.7965 (ptp) cc_final: 0.7739 (pmm) REVERT: K 300 LEU cc_start: 0.9301 (mt) cc_final: 0.9087 (mt) REVERT: K 912 LEU cc_start: 0.8310 (mm) cc_final: 0.8076 (mm) REVERT: K 1070 HIS cc_start: 0.9150 (t-90) cc_final: 0.8398 (t70) REVERT: K 1120 MET cc_start: 0.9055 (mmp) cc_final: 0.8213 (tmm) REVERT: K 1127 ASP cc_start: 0.8848 (m-30) cc_final: 0.8597 (p0) outliers start: 1 outliers final: 0 residues processed: 472 average time/residue: 0.3777 time to fit residues: 263.4303 Evaluate side-chains 413 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [64, 3, 159, 81, 158, 124, 147, 137, 135, 151, 112] chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 ASN ** L 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN G 69 ASN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.043215 restraints weight = 281613.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.046609 restraints weight = 122335.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048792 restraints weight = 66322.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050262 restraints weight = 41860.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051217 restraints weight = 29732.537| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 22501 Z= 0.294 Angle : 0.758 11.989 31656 Z= 0.449 Chirality : 0.059 1.656 3575 Planarity : 0.006 0.068 3041 Dihedral : 28.434 179.015 5424 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.40 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.17), residues: 1952 helix: -0.12 (0.18), residues: 657 sheet: -1.32 (0.25), residues: 416 loop : -1.83 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 41 TYR 0.038 0.002 TYR F 52 PHE 0.037 0.002 PHE K 975 TRP 0.009 0.002 TRP L 320 HIS 0.008 0.002 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.29 (22501) covalent geometry : angle 0.75777 / 0.45 (31656) hydrogen bonds : bond 0.07374 / 8.05 ( 1081) hydrogen bonds : angle 5.63556 / 7.23 ( 2806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 177 MET cc_start: 0.9199 (tmm) cc_final: 0.8981 (tmm) REVERT: L 250 LEU cc_start: 0.7966 (mm) cc_final: 0.7748 (mm) REVERT: L 299 ASP cc_start: 0.9072 (t0) cc_final: 0.8784 (t0) REVERT: A 57 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9265 (tppt) REVERT: A 106 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8982 (tm-30) REVERT: A 124 ASP cc_start: 0.8845 (m-30) cc_final: 0.8606 (m-30) REVERT: B 65 ASN cc_start: 0.9528 (m110) cc_final: 0.9244 (m110) REVERT: D 35 LYS cc_start: 0.8723 (mppt) cc_final: 0.8405 (mmtm) REVERT: D 36 GLU cc_start: 0.5982 (pp20) cc_final: 0.3604 (mm-30) REVERT: D 68 ASN cc_start: 0.8971 (m-40) cc_final: 0.8429 (t0) REVERT: D 72 GLU cc_start: 0.8786 (pt0) cc_final: 0.8493 (pt0) REVERT: D 90 ILE cc_start: 0.9440 (tt) cc_final: 0.9152 (tp) REVERT: D 93 ARG cc_start: 0.9543 (ttm170) cc_final: 0.9314 (ttm-80) REVERT: D 94 GLU cc_start: 0.9552 (mp0) cc_final: 0.9178 (mp0) REVERT: D 96 GLN cc_start: 0.9572 (tt0) cc_final: 0.9050 (tm-30) REVERT: D 114 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9178 (mm-30) REVERT: E 71 LEU cc_start: 0.9645 (tp) cc_final: 0.9309 (mm) REVERT: E 79 PHE cc_start: 0.9288 (m-80) cc_final: 0.8858 (m-80) REVERT: E 98 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9204 (mt-10) REVERT: E 119 THR cc_start: 0.8891 (m) cc_final: 0.8628 (m) REVERT: E 121 MET cc_start: 0.8387 (mtp) cc_final: 0.7918 (mtp) REVERT: E 124 ASP cc_start: 0.9404 (m-30) cc_final: 0.9037 (m-30) REVERT: E 134 GLU cc_start: 0.7315 (tp30) cc_final: 0.6652 (tp30) REVERT: F 54 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8784 (mm-30) REVERT: F 65 ASN cc_start: 0.9441 (m-40) cc_final: 0.9132 (m-40) REVERT: G 40 TYR cc_start: 0.8861 (m-80) cc_final: 0.8484 (m-80) REVERT: G 103 ILE cc_start: 0.9385 (mm) cc_final: 0.8843 (tp) REVERT: H 58 LYS cc_start: 0.9267 (mtpt) cc_final: 0.8950 (mmmm) REVERT: H 85 ASN cc_start: 0.8980 (m110) cc_final: 0.8778 (m110) REVERT: H 114 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9383 (mm-30) REVERT: H 117 LYS cc_start: 0.9824 (ttpt) cc_final: 0.9505 (tmtt) REVERT: K 60 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8826 (tptt) REVERT: K 130 MET cc_start: 0.8007 (ptp) cc_final: 0.7755 (pmm) REVERT: K 300 LEU cc_start: 0.9327 (mt) cc_final: 0.9101 (mt) REVERT: K 1070 HIS cc_start: 0.9182 (t-90) cc_final: 0.8435 (t70) REVERT: K 1120 MET cc_start: 0.9057 (mmp) cc_final: 0.8230 (tmm) REVERT: K 1127 ASP cc_start: 0.8873 (m-30) cc_final: 0.8623 (p0) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.3769 time to fit residues: 257.9824 Evaluate side-chains 408 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [181, 182, 26, 36, 4, 46, 143, 119, 116, 32, 194] chunk 181 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 87 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 ASN ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 398 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 GLN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045820 restraints weight = 256675.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049524 restraints weight = 108416.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051941 restraints weight = 57628.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.053516 restraints weight = 35589.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054558 restraints weight = 24844.702| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22501 Z= 0.145 Angle : 0.673 11.440 31656 Z= 0.398 Chirality : 0.059 1.624 3575 Planarity : 0.005 0.055 3041 Dihedral : 28.479 178.793 5424 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 0.06 % Allowed : 0.12 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.18), residues: 1952 helix: 0.72 (0.19), residues: 662 sheet: -1.24 (0.25), residues: 413 loop : -1.70 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 37 TYR 0.029 0.002 TYR F 52 PHE 0.016 0.002 PHE L 257 TRP 0.013 0.002 TRP L 320 HIS 0.009 0.001 HIS L 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (22501) covalent geometry : angle 0.67277 / 0.40 (31656) hydrogen bonds : bond 0.05527 / 5.99 ( 1081) hydrogen bonds : angle 4.88252 / 6.30 ( 2806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 123 is missing expected H atoms. Skipping. Evaluate side-chains 476 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 177 MET cc_start: 0.9168 (tmm) cc_final: 0.8947 (tmm) REVERT: L 255 ASP cc_start: 0.8248 (p0) cc_final: 0.7907 (p0) REVERT: L 299 ASP cc_start: 0.9000 (t0) cc_final: 0.8706 (t0) REVERT: L 348 TYR cc_start: 0.7911 (m-80) cc_final: 0.7597 (m-80) REVERT: A 91 MET cc_start: 0.9639 (mtp) cc_final: 0.9417 (mtp) REVERT: A 106 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8702 (tm-30) REVERT: B 35 ILE cc_start: 0.9700 (mm) cc_final: 0.9469 (tt) REVERT: B 65 ASN cc_start: 0.9477 (m110) cc_final: 0.9273 (m110) REVERT: D 35 LYS cc_start: 0.8626 (mppt) cc_final: 0.8366 (mmtm) REVERT: D 36 GLU cc_start: 0.5724 (pp20) cc_final: 0.3428 (mm-30) REVERT: D 68 ASN cc_start: 0.8859 (m-40) cc_final: 0.8342 (t0) REVERT: D 72 GLU cc_start: 0.8690 (pt0) cc_final: 0.8366 (pt0) REVERT: D 90 ILE cc_start: 0.9338 (tt) cc_final: 0.8962 (tp) REVERT: D 93 ARG cc_start: 0.9530 (ttm170) cc_final: 0.9307 (ttm-80) REVERT: D 94 GLU cc_start: 0.9569 (mp0) cc_final: 0.9203 (mp0) REVERT: D 114 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9117 (mm-30) REVERT: D 117 LYS cc_start: 0.9571 (ptpp) cc_final: 0.9316 (ptpp) REVERT: D 121 LYS cc_start: 0.9545 (mtpt) cc_final: 0.9080 (tppt) REVERT: E 79 PHE cc_start: 0.9204 (m-80) cc_final: 0.8830 (m-80) REVERT: E 91 MET cc_start: 0.9434 (mmp) cc_final: 0.9196 (mmm) REVERT: E 98 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9195 (mt-10) REVERT: E 134 GLU cc_start: 0.7106 (tp30) cc_final: 0.6452 (tp30) REVERT: F 51 ILE cc_start: 0.9478 (mm) cc_final: 0.9222 (mm) REVERT: F 53 GLU cc_start: 0.9000 (pm20) cc_final: 0.8607 (pm20) REVERT: F 54 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8616 (mm-30) REVERT: F 65 ASN cc_start: 0.9387 (m-40) cc_final: 0.9062 (m110) REVERT: G 18 ARG cc_start: 0.8569 (mtt180) cc_final: 0.8309 (mtp180) REVERT: G 103 ILE cc_start: 0.9340 (mm) cc_final: 0.8796 (tp) REVERT: H 58 LYS cc_start: 0.9206 (mtpt) cc_final: 0.8875 (mmmm) REVERT: H 68 ASN cc_start: 0.8505 (m110) cc_final: 0.8220 (m-40) REVERT: H 83 HIS cc_start: 0.8860 (t-170) cc_final: 0.8650 (t70) REVERT: H 93 ARG cc_start: 0.9316 (mtp-110) cc_final: 0.8728 (ptm-80) REVERT: H 114 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9278 (mm-30) REVERT: H 117 LYS cc_start: 0.9811 (ttpt) cc_final: 0.9462 (tmtt) REVERT: K 60 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8776 (tptt) REVERT: K 130 MET cc_start: 0.8002 (ptp) cc_final: 0.7752 (pmm) REVERT: K 300 LEU cc_start: 0.9306 (mt) cc_final: 0.9064 (mt) REVERT: K 1070 HIS cc_start: 0.9150 (t-90) cc_final: 0.8382 (t70) REVERT: K 1120 MET cc_start: 0.9058 (mmp) cc_final: 0.8215 (tmm) REVERT: K 1127 ASP cc_start: 0.8816 (m-30) cc_final: 0.8556 (p0) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.3791 time to fit residues: 263.7533 Evaluate side-chains 416 residues out of total 1689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: [102, 198, 189, 141, 22, 104, 175, 16, 172, 54, 214] chunk 102 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 292 ASN ** L 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN E 86 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN K 826 ASN ** K 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042143 restraints weight = 279215.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045553 restraints weight = 118701.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047759 restraints weight = 63894.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049223 restraints weight = 39937.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050182 restraints weight = 28197.277| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.161 22501 Z= 0.351 Angle : 0.822 11.910 31656 Z= 0.481 Chirality : 0.059 1.622 3575 Planarity : 0.006 0.089 3041 Dihedral : 28.544 179.485 5424 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.61 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 1952 helix: -0.45 (0.18), residues: 655 sheet: -1.40 (0.25), residues: 418 loop : -1.93 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 41 TYR 0.030 0.003 TYR H 84 PHE 0.037 0.003 PHE F 101 TRP 0.012 0.002 TRP L 270 HIS 0.015 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.35 (22501) covalent geometry : angle 0.82173 / 0.48 (31656) hydrogen bonds : bond 0.08477 / 9.28 ( 1081) hydrogen bonds : angle 5.85679 / 7.50 ( 2806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7587.00 seconds wall clock time: 129 minutes 51.27 seconds (7791.27 seconds total)