Starting phenix.real_space_refine on Wed Mar 4 21:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s85_10116/03_2026/6s85_10116.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4320 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 67 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 7987 2.51 5 N 2293 2.21 5 O 2631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13018 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2916 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 7, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2923 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 7, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3010 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2816 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 4 Chain: "E" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 659 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 21 residue: pdb=" N GLY A 284 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY A 284 " occ=0.50 residue: pdb=" N ALA A 287 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 287 " occ=0.60 residue: pdb=" N THR A 290 " occ=0.70 ... (5 atoms not shown) pdb=" CG2 THR A 290 " occ=0.70 residue: pdb=" N ALA A 291 " occ=0.60 ... (3 atoms not shown) pdb=" CB ALA A 291 " occ=0.60 residue: pdb=" N GLN A 292 " occ=0.70 ... (7 atoms not shown) pdb=" NE2 GLN A 292 " occ=0.70 residue: pdb=" N LEU A 293 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 293 " occ=0.80 residue: pdb=" N PRO A 303 " occ=0.61 ... (5 atoms not shown) pdb=" CD PRO A 303 " occ=0.61 residue: pdb=" N PRO A 304 " occ=0.68 ... (5 atoms not shown) pdb=" CD PRO A 304 " occ=0.68 residue: pdb=" N VAL A 305 " occ=0.88 ... (5 atoms not shown) pdb=" CG2 VAL A 305 " occ=0.88 residue: pdb=" N TRP A 306 " occ=0.97 ... (12 atoms not shown) pdb=" CH2 TRP A 306 " occ=0.97 residue: pdb=" N LEU A 307 " occ=0.87 ... (6 atoms not shown) pdb=" CD2 LEU A 307 " occ=0.87 residue: pdb=" N ILE A 309 " occ=0.89 ... (6 atoms not shown) pdb=" CD1 ILE A 309 " occ=0.89 ... (remaining 9 not shown) Time building chain proxies: 2.85, per 1000 atoms: 0.22 Number of scatterers: 13018 At special positions: 0 Unit cell: (95.12, 102.5, 145.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 34 16.00 P 67 15.00 Mg 2 11.99 O 2631 8.00 N 2293 7.00 C 7987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 558.1 milliseconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 16 sheets defined 39.4% alpha, 13.5% beta 27 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.620A pdb=" N LEU C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 104 Processing helix chain 'C' and resid 128 through 141 removed outlier: 4.186A pdb=" N GLU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 removed outlier: 3.656A pdb=" N ARG C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 removed outlier: 3.576A pdb=" N THR C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 removed outlier: 5.032A pdb=" N SER C 186 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 876 through 881 removed outlier: 4.416A pdb=" N TRP C 880 " --> pdb=" O GLN C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 887 Processing helix chain 'C' and resid 893 through 917 removed outlier: 4.432A pdb=" N LEU C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASP C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N HIS C 909 " --> pdb=" O ASP C 905 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 910 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 969 Processing helix chain 'C' and resid 992 through 1005 removed outlier: 4.058A pdb=" N THR C 996 " --> pdb=" O GLU C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1024 Processing helix chain 'D' and resid 24 through 29 Processing helix chain 'D' and resid 42 through 56 removed outlier: 4.562A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.511A pdb=" N PHE D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 4.683A pdb=" N LEU D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 177 removed outlier: 4.443A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 199 removed outlier: 4.449A pdb=" N ALA D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 885 Processing helix chain 'D' and resid 892 through 919 removed outlier: 3.747A pdb=" N ARG D 896 " --> pdb=" O GLY D 892 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN D 913 " --> pdb=" O HIS D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 951 removed outlier: 3.627A pdb=" N THR D 950 " --> pdb=" O ASP D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 971 removed outlier: 3.902A pdb=" N VAL D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 989 Processing helix chain 'D' and resid 993 through 1007 removed outlier: 3.738A pdb=" N ALA D1003 " --> pdb=" O ASP D 999 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.781A pdb=" N PHE A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.775A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.727A pdb=" N LEU A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.721A pdb=" N ALA A 98 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.645A pdb=" N ILE A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.813A pdb=" N LYS A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 319 through 328 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.776A pdb=" N ARG A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 377 through 393 removed outlier: 4.069A pdb=" N HIS A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.686A pdb=" N HIS B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.521A pdb=" N LEU B 62 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLN B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 152 through 173 removed outlier: 3.889A pdb=" N ILE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR B 161 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.654A pdb=" N PHE B 212 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.654A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 316 through 331 removed outlier: 3.892A pdb=" N GLN B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG B 322 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 369 removed outlier: 3.554A pdb=" N VAL B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 394 removed outlier: 3.584A pdb=" N THR B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 389 " --> pdb=" O HIS B 385 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 21 removed outlier: 6.426A pdb=" N GLU C 84 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 6 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU C 82 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 8 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 80 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 979 through 982 removed outlier: 5.809A pdb=" N PHE C 33 " --> pdb=" O VAL C1013 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 922 through 926 removed outlier: 3.598A pdb=" N ARG C 946 " --> pdb=" O VAL C 936 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.129A pdb=" N ILE D 3 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU D 86 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.434A pdb=" N PHE D 33 " --> pdb=" O VAL D1013 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU D 980 " --> pdb=" O GLY D1012 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE D1014 " --> pdb=" O LEU D 980 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 982 " --> pdb=" O ILE D1014 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 922 through 926 Processing sheet with id=AA7, first strand: chain 'D' and resid 1030 through 1032 Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105 removed outlier: 7.561A pdb=" N LEU A 77 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL A 105 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 79 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 4 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA A 46 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 6 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 255 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 271 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 261 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.535A pdb=" N GLN A 113 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE A 179 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA A 219 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA A 181 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 236 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL A 235 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 229 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 279 through 282 removed outlier: 6.746A pdb=" N ALA A 280 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLU A 310 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 282 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU A 336 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 307 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 338 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 309 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 340 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 311 " --> pdb=" O ARG A 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.334A pdb=" N ILE B 43 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 77 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 113 through 116 removed outlier: 7.078A pdb=" N GLN B 113 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N VAL B 125 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 115 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE B 180 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 125 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB5, first strand: chain 'B' and resid 254 through 261 removed outlier: 6.008A pdb=" N VAL B 255 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 270 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 257 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 268 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR B 259 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 279 through 280 removed outlier: 5.758A pdb=" N VAL B 305 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.592A pdb=" N ILE B 309 " --> pdb=" O ARG B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 403 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3340 1.33 - 1.45: 2779 1.45 - 1.57: 7078 1.57 - 1.69: 130 1.69 - 1.81: 52 Bond restraints: 13379 Sorted by residual: bond pdb=" C SER C 67 " pdb=" N GLN C 68 " ideal model delta sigma weight residual 1.333 1.397 -0.064 1.29e-02 6.01e+03 2.49e+01 bond pdb=" N VAL C 114 " pdb=" CA VAL C 114 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.11e-02 8.12e+03 1.30e+01 bond pdb=" N GLN C 155 " pdb=" CA GLN C 155 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.28e-02 6.10e+03 1.17e+01 bond pdb=" N THR D 177 " pdb=" CA THR D 177 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.22e-02 6.72e+03 9.63e+00 bond pdb=" N LYS D 894 " pdb=" CA LYS D 894 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.09e+00 ... (remaining 13374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 18204 3.39 - 6.78: 191 6.78 - 10.18: 16 10.18 - 13.57: 1 13.57 - 16.96: 3 Bond angle restraints: 18415 Sorted by residual: angle pdb=" N SER D 889 " pdb=" CA SER D 889 " pdb=" C SER D 889 " ideal model delta sigma weight residual 113.55 128.16 -14.61 1.26e+00 6.30e-01 1.34e+02 angle pdb=" N LYS D 890 " pdb=" CA LYS D 890 " pdb=" C LYS D 890 " ideal model delta sigma weight residual 109.24 92.28 16.96 1.67e+00 3.59e-01 1.03e+02 angle pdb=" C SER D 889 " pdb=" CA SER D 889 " pdb=" CB SER D 889 " ideal model delta sigma weight residual 109.34 94.92 14.42 1.55e+00 4.16e-01 8.66e+01 angle pdb=" O3' DG F 70 " pdb=" C3' DG F 70 " pdb=" C2' DG F 70 " ideal model delta sigma weight residual 111.50 101.35 10.15 1.50e+00 4.44e-01 4.58e+01 angle pdb=" N SER C 154 " pdb=" CA SER C 154 " pdb=" C SER C 154 " ideal model delta sigma weight residual 110.55 117.57 -7.02 1.35e+00 5.49e-01 2.71e+01 ... (remaining 18410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 6491 16.64 - 33.29: 858 33.29 - 49.93: 387 49.93 - 66.58: 129 66.58 - 83.22: 30 Dihedral angle restraints: 7895 sinusoidal: 3592 harmonic: 4303 Sorted by residual: dihedral pdb=" CD ARG D 946 " pdb=" NE ARG D 946 " pdb=" CZ ARG D 946 " pdb=" NH1 ARG D 946 " ideal model delta sinusoidal sigma weight residual 0.00 -74.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" C ASP B 376 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " pdb=" CB ASP B 376 " ideal model delta harmonic sigma weight residual -122.60 -137.83 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA GLU C 25 " pdb=" C GLU C 25 " pdb=" N PRO C 26 " pdb=" CA PRO C 26 " ideal model delta harmonic sigma weight residual 180.00 151.94 28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 7892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1882 0.094 - 0.189: 222 0.189 - 0.283: 14 0.283 - 0.377: 1 0.377 - 0.472: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CA ASP B 376 " pdb=" N ASP B 376 " pdb=" C ASP B 376 " pdb=" CB ASP B 376 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CA ASP D 893 " pdb=" N ASP D 893 " pdb=" C ASP D 893 " pdb=" CB ASP D 893 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA GLU B 302 " pdb=" N GLU B 302 " pdb=" C GLU B 302 " pdb=" CB GLU B 302 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2117 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 946 " -1.060 9.50e-02 1.11e+02 4.75e-01 1.36e+02 pdb=" NE ARG D 946 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG D 946 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 946 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 946 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 248 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU B 248 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU B 248 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS B 249 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D1028 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C ILE D1028 " -0.046 2.00e-02 2.50e+03 pdb=" O ILE D1028 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS D1029 " 0.015 2.00e-02 2.50e+03 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 94 2.40 - 3.03: 6972 3.03 - 3.65: 20541 3.65 - 4.28: 29819 4.28 - 4.90: 46689 Nonbonded interactions: 104115 Sorted by model distance: nonbonded pdb=" OP1 DG F 76 " pdb="MN MN A 501 " model vdw 1.775 2.320 nonbonded pdb=" O PHE B 246 " pdb=" SG CYS B 249 " model vdw 1.782 3.400 nonbonded pdb=" OD2 ASP A 48 " pdb="MN MN A 501 " model vdw 1.808 2.320 nonbonded pdb=" CB PHE D 190 " pdb=" O SER D 889 " model vdw 1.823 3.440 nonbonded pdb=" OD2 ASP B 48 " pdb="MN MN B 502 " model vdw 1.836 2.320 ... (remaining 104110 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' and (resid 1 through 105 or resid 109 through 137 or resid 151 throug \ h 188 or resid 205 through 342 or resid 354 through 502)) selection = (chain 'B' and (resid 1 through 188 or resid 205 through 502)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 201 or resid 875 through 1102)) } 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=0.28 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.008 0.064 13379 Z= 0.435 Angle : 1.013 16.962 18415 Z= 0.614 Chirality : 0.060 0.472 2120 Planarity : 0.012 0.475 2153 Dihedral : 19.276 83.221 5101 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.79 % Favored : 91.87 % Rotamer: Outliers : 1.03 % Allowed : 12.07 % Favored : 86.91 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % 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: -3.59 (0.19), residues: 1464 helix: -2.64 (0.19), residues: 479 sheet: -2.41 (0.29), residues: 269 loop : -2.08 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 917 TYR 0.012 0.002 TYR A 161 PHE 0.018 0.002 PHE B 260 TRP 0.016 0.002 TRP C 880 HIS 0.009 0.002 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00784 (13379) covalent geometry : angle 1.01268 (18415) hydrogen bonds : bond 0.21011 ( 469) hydrogen bonds : angle 8.42770 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.465 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: D 188 MET cc_start: 0.8640 (ttp) cc_final: 0.8148 (tmm) REVERT: D 889 SER cc_start: 0.6878 (p) cc_final: 0.6511 (p) REVERT: D 900 GLN cc_start: 0.7946 (mm110) cc_final: 0.7636 (mm-40) REVERT: D 930 GLU cc_start: 0.8237 (pt0) cc_final: 0.7867 (mp0) REVERT: D 967 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8317 (tt) REVERT: D 990 ASP cc_start: 0.8407 (p0) cc_final: 0.7767 (p0) REVERT: A 254 TYR cc_start: 0.8735 (m-80) cc_final: 0.8378 (m-10) REVERT: B 170 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8369 (mmtm) REVERT: B 217 TYR cc_start: 0.8943 (t80) cc_final: 0.8565 (t80) REVERT: B 292 GLN cc_start: 0.8607 (mt0) cc_final: 0.8338 (mt0) outliers start: 13 outliers final: 4 residues processed: 191 average time/residue: 0.1309 time to fit residues: 34.6503 Evaluate side-chains 117 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0040 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 0.8332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 103 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN C 941 GLN C1005 ASN D 875 GLN D 900 GLN A 277 GLN B 71 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.079514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.064446 restraints weight = 47439.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066112 restraints weight = 29980.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067266 restraints weight = 21391.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067969 restraints weight = 16739.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068575 restraints weight = 14157.367| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13379 Z= 0.130 Angle : 0.619 7.749 18415 Z= 0.327 Chirality : 0.041 0.219 2120 Planarity : 0.004 0.043 2153 Dihedral : 19.569 89.573 2313 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.40 (0.21), residues: 1464 helix: -1.22 (0.21), residues: 508 sheet: -2.05 (0.30), residues: 263 loop : -1.57 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 382 TYR 0.016 0.001 TYR B 63 PHE 0.017 0.001 PHE C 986 TRP 0.013 0.001 TRP D 96 HIS 0.006 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00281 (13379) covalent geometry : angle 0.61885 (18415) hydrogen bonds : bond 0.04207 ( 469) hydrogen bonds : angle 5.13629 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.521 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: C 98 GLN cc_start: 0.8387 (tt0) cc_final: 0.8120 (tt0) REVERT: C 146 ARG cc_start: 0.8819 (mpp80) cc_final: 0.8472 (mpp80) REVERT: C 197 ARG cc_start: 0.8547 (mmt180) cc_final: 0.7593 (mmp-170) REVERT: C 950 THR cc_start: 0.9416 (p) cc_final: 0.9196 (t) REVERT: D 188 MET cc_start: 0.8534 (ttp) cc_final: 0.7993 (tmm) REVERT: D 889 SER cc_start: 0.8501 (p) cc_final: 0.8119 (p) REVERT: D 990 ASP cc_start: 0.7832 (p0) cc_final: 0.7291 (p0) REVERT: A 254 TYR cc_start: 0.8543 (m-80) cc_final: 0.8119 (m-10) REVERT: B 170 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8129 (mmtm) REVERT: B 217 TYR cc_start: 0.8637 (t80) cc_final: 0.8334 (t80) REVERT: B 306 TRP cc_start: 0.9190 (m-10) cc_final: 0.8763 (m-10) REVERT: B 366 PHE cc_start: 0.9139 (t80) cc_final: 0.8605 (t80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1108 time to fit residues: 29.8298 Evaluate side-chains 115 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 0.0030 chunk 111 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 127 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1016 HIS A 38 HIS A 152 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.078179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.062899 restraints weight = 48324.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.064628 restraints weight = 29818.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065830 restraints weight = 20904.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066668 restraints weight = 16145.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067217 restraints weight = 13348.411| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13379 Z= 0.115 Angle : 0.580 6.406 18415 Z= 0.304 Chirality : 0.040 0.182 2120 Planarity : 0.003 0.034 2153 Dihedral : 19.143 83.846 2313 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.22), residues: 1464 helix: -0.47 (0.22), residues: 501 sheet: -1.77 (0.30), residues: 263 loop : -1.28 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.019 0.001 TYR B 16 PHE 0.015 0.001 PHE A 27 TRP 0.008 0.001 TRP D 96 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00250 (13379) covalent geometry : angle 0.57986 (18415) hydrogen bonds : bond 0.03549 ( 469) hydrogen bonds : angle 4.68117 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 TYR cc_start: 0.8286 (m-80) cc_final: 0.8084 (m-10) REVERT: C 98 GLN cc_start: 0.8356 (tt0) cc_final: 0.8086 (tt0) REVERT: C 197 ARG cc_start: 0.8491 (mmt180) cc_final: 0.7485 (mmp-170) REVERT: D 11 LEU cc_start: 0.9163 (mm) cc_final: 0.8953 (mm) REVERT: D 151 MET cc_start: 0.7905 (tpt) cc_final: 0.7685 (tpt) REVERT: D 175 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8076 (mm-30) REVERT: D 188 MET cc_start: 0.8602 (ttp) cc_final: 0.8040 (tmm) REVERT: D 889 SER cc_start: 0.8337 (p) cc_final: 0.7935 (p) REVERT: D 990 ASP cc_start: 0.7809 (p0) cc_final: 0.7288 (p0) REVERT: A 89 THR cc_start: 0.8328 (m) cc_final: 0.7934 (p) REVERT: A 254 TYR cc_start: 0.8659 (m-80) cc_final: 0.8230 (m-10) REVERT: A 323 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8454 (mttp) REVERT: B 170 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8181 (mmtm) REVERT: B 217 TYR cc_start: 0.8735 (t80) cc_final: 0.8458 (t80) REVERT: B 306 TRP cc_start: 0.9234 (m-10) cc_final: 0.8773 (m-10) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1089 time to fit residues: 26.5564 Evaluate side-chains 111 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS A 110 HIS A 318 HIS B 36 GLN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** 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 = 0.3377 r_free = 0.3377 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058934 restraints weight = 50088.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060580 restraints weight = 31076.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061774 restraints weight = 21962.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062585 restraints weight = 16957.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063189 restraints weight = 14097.756| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13379 Z= 0.238 Angle : 0.676 6.851 18415 Z= 0.352 Chirality : 0.043 0.175 2120 Planarity : 0.004 0.031 2153 Dihedral : 19.188 81.294 2313 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.59 (0.22), residues: 1464 helix: -0.22 (0.22), residues: 511 sheet: -1.98 (0.30), residues: 250 loop : -1.24 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 146 TYR 0.016 0.002 TYR B 16 PHE 0.022 0.002 PHE B 246 TRP 0.015 0.001 TRP D 940 HIS 0.010 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00511 (13379) covalent geometry : angle 0.67646 (18415) hydrogen bonds : bond 0.04589 ( 469) hydrogen bonds : angle 4.83603 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 ASN cc_start: 0.8508 (t0) cc_final: 0.8255 (t0) REVERT: D 188 MET cc_start: 0.8842 (ttp) cc_final: 0.8501 (ppp) REVERT: D 889 SER cc_start: 0.8644 (p) cc_final: 0.8152 (p) REVERT: D 900 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8103 (mm-40) REVERT: D 983 ASP cc_start: 0.8015 (t70) cc_final: 0.7643 (t0) REVERT: D 990 ASP cc_start: 0.8048 (p0) cc_final: 0.7498 (p0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0975 time to fit residues: 18.5946 Evaluate side-chains 98 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.061189 restraints weight = 49069.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062867 restraints weight = 30418.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064055 restraints weight = 21426.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064884 restraints weight = 16573.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065389 restraints weight = 13711.824| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13379 Z= 0.126 Angle : 0.574 6.780 18415 Z= 0.299 Chirality : 0.040 0.141 2120 Planarity : 0.003 0.029 2153 Dihedral : 18.941 79.903 2313 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.22), residues: 1464 helix: 0.01 (0.23), residues: 514 sheet: -1.75 (0.30), residues: 265 loop : -1.02 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 60 TYR 0.025 0.001 TYR A 316 PHE 0.029 0.001 PHE A 366 TRP 0.009 0.001 TRP C 880 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00275 (13379) covalent geometry : angle 0.57397 (18415) hydrogen bonds : bond 0.03369 ( 469) hydrogen bonds : angle 4.53736 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 MET cc_start: 0.8364 (ptm) cc_final: 0.8088 (ptm) REVERT: C 149 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8139 (mtp85) REVERT: C 197 ARG cc_start: 0.8488 (mmt180) cc_final: 0.7531 (mmp-170) REVERT: D 188 MET cc_start: 0.8774 (ttp) cc_final: 0.8498 (ppp) REVERT: D 889 SER cc_start: 0.8649 (p) cc_final: 0.8178 (p) REVERT: D 990 ASP cc_start: 0.7946 (p0) cc_final: 0.7457 (p0) REVERT: B 306 TRP cc_start: 0.9271 (m-10) cc_final: 0.8763 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0991 time to fit residues: 21.1400 Evaluate side-chains 110 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 24 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 88 optimal weight: 0.0040 chunk 115 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 256 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.076270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060945 restraints weight = 48960.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062671 restraints weight = 30075.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063881 restraints weight = 21064.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.064660 restraints weight = 16192.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065277 restraints weight = 13448.967| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13379 Z= 0.140 Angle : 0.579 6.617 18415 Z= 0.300 Chirality : 0.040 0.143 2120 Planarity : 0.003 0.031 2153 Dihedral : 18.817 77.137 2313 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 0.08 % Allowed : 2.52 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.23), residues: 1464 helix: 0.25 (0.23), residues: 513 sheet: -1.75 (0.31), residues: 265 loop : -0.95 (0.26), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.023 0.001 TYR A 316 PHE 0.010 0.001 PHE A 27 TRP 0.008 0.001 TRP D 940 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00308 (13379) covalent geometry : angle 0.57902 (18415) hydrogen bonds : bond 0.03402 ( 469) hydrogen bonds : angle 4.46389 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.8575 (tt0) cc_final: 0.8287 (tt0) REVERT: C 149 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8184 (mtp85) REVERT: C 197 ARG cc_start: 0.8423 (mmt180) cc_final: 0.7506 (mmp-170) REVERT: D 188 MET cc_start: 0.8789 (ttp) cc_final: 0.8509 (ppp) REVERT: D 889 SER cc_start: 0.8698 (p) cc_final: 0.8210 (p) REVERT: D 990 ASP cc_start: 0.7907 (p0) cc_final: 0.7446 (p0) REVERT: B 97 MET cc_start: 0.8563 (mtt) cc_final: 0.8335 (mtp) REVERT: B 306 TRP cc_start: 0.9277 (m-10) cc_final: 0.8796 (m-10) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1057 time to fit residues: 22.2047 Evaluate side-chains 100 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 36 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059288 restraints weight = 49510.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060946 restraints weight = 30827.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062128 restraints weight = 21812.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062889 restraints weight = 16889.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063502 restraints weight = 14086.138| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13379 Z= 0.205 Angle : 0.638 8.887 18415 Z= 0.330 Chirality : 0.042 0.191 2120 Planarity : 0.004 0.032 2153 Dihedral : 18.816 79.308 2313 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.22), residues: 1464 helix: 0.34 (0.23), residues: 507 sheet: -1.84 (0.32), residues: 242 loop : -0.98 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.019 0.002 TYR A 316 PHE 0.017 0.002 PHE A 212 TRP 0.015 0.001 TRP D 940 HIS 0.007 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00444 (13379) covalent geometry : angle 0.63817 (18415) hydrogen bonds : bond 0.04000 ( 469) hydrogen bonds : angle 4.63073 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.8638 (tt0) cc_final: 0.8308 (tt0) REVERT: C 149 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8150 (mtp85) REVERT: D 188 MET cc_start: 0.8803 (ttp) cc_final: 0.8485 (ppp) REVERT: D 889 SER cc_start: 0.8858 (p) cc_final: 0.8386 (p) REVERT: D 900 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8073 (mm-40) REVERT: D 983 ASP cc_start: 0.7846 (t70) cc_final: 0.7535 (t0) REVERT: D 990 ASP cc_start: 0.8016 (p0) cc_final: 0.7517 (p0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1130 time to fit residues: 21.9135 Evaluate side-chains 99 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 0.0030 chunk 73 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.3948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.078066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062665 restraints weight = 47939.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.064415 restraints weight = 29358.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065667 restraints weight = 20536.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.066475 restraints weight = 15747.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.067084 restraints weight = 13062.038| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13379 Z= 0.106 Angle : 0.566 7.512 18415 Z= 0.289 Chirality : 0.040 0.177 2120 Planarity : 0.003 0.034 2153 Dihedral : 18.535 73.776 2313 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.23), residues: 1464 helix: 0.61 (0.23), residues: 512 sheet: -1.60 (0.32), residues: 255 loop : -0.87 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 149 TYR 0.021 0.001 TYR A 316 PHE 0.009 0.001 PHE C 986 TRP 0.012 0.001 TRP C 880 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00227 (13379) covalent geometry : angle 0.56613 (18415) hydrogen bonds : bond 0.02920 ( 469) hydrogen bonds : angle 4.29980 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 ARG cc_start: 0.8459 (mmt180) cc_final: 0.7543 (mmp-170) REVERT: D 18 TRP cc_start: 0.7380 (m100) cc_final: 0.7147 (m100) REVERT: D 188 MET cc_start: 0.8651 (ttp) cc_final: 0.8448 (ppp) REVERT: D 889 SER cc_start: 0.8664 (p) cc_final: 0.8203 (p) REVERT: D 990 ASP cc_start: 0.7926 (p0) cc_final: 0.7484 (p0) REVERT: A 254 TYR cc_start: 0.8658 (m-80) cc_final: 0.8334 (m-10) REVERT: B 306 TRP cc_start: 0.9206 (m-10) cc_final: 0.8924 (m-10) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1064 time to fit residues: 24.0120 Evaluate side-chains 109 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 43 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.058994 restraints weight = 49688.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060737 restraints weight = 30476.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.061960 restraints weight = 21335.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.062820 restraints weight = 16392.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063422 restraints weight = 13532.350| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3104 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3104 r_free = 0.3104 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3104 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13379 Z= 0.228 Angle : 0.659 9.257 18415 Z= 0.339 Chirality : 0.042 0.159 2120 Planarity : 0.004 0.032 2153 Dihedral : 18.714 80.190 2313 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.23), residues: 1464 helix: 0.39 (0.23), residues: 515 sheet: -1.76 (0.32), residues: 242 loop : -0.89 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 113 TYR 0.023 0.002 TYR A 161 PHE 0.014 0.002 PHE D 898 TRP 0.016 0.002 TRP D 940 HIS 0.008 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00493 (13379) covalent geometry : angle 0.65890 (18415) hydrogen bonds : bond 0.04129 ( 469) hydrogen bonds : angle 4.61662 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 ARG cc_start: 0.8377 (mtt90) cc_final: 0.8172 (mtp85) REVERT: D 188 MET cc_start: 0.8794 (ttp) cc_final: 0.8478 (ppp) REVERT: D 889 SER cc_start: 0.8917 (p) cc_final: 0.8447 (p) REVERT: D 900 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8095 (mm-40) REVERT: D 990 ASP cc_start: 0.8096 (p0) cc_final: 0.7506 (p0) REVERT: A 165 TYR cc_start: 0.8712 (t80) cc_final: 0.8508 (t80) REVERT: B 306 TRP cc_start: 0.9250 (m-10) cc_final: 0.8873 (m-10) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.0991 time to fit residues: 18.6847 Evaluate side-chains 94 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.073906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058775 restraints weight = 48958.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060441 restraints weight = 30309.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061570 restraints weight = 21336.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062411 restraints weight = 16500.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.063037 restraints weight = 13648.534| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13379 Z= 0.232 Angle : 0.667 9.622 18415 Z= 0.345 Chirality : 0.043 0.178 2120 Planarity : 0.004 0.034 2153 Dihedral : 18.739 78.935 2313 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.22), residues: 1464 helix: 0.28 (0.23), residues: 514 sheet: -1.91 (0.32), residues: 247 loop : -0.92 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 946 TYR 0.016 0.002 TYR A 316 PHE 0.021 0.002 PHE A 366 TRP 0.018 0.001 TRP D 940 HIS 0.008 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00500 (13379) covalent geometry : angle 0.66667 (18415) hydrogen bonds : bond 0.04035 ( 469) hydrogen bonds : angle 4.67859 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 149 ARG cc_start: 0.8370 (mtt90) cc_final: 0.8170 (mtp85) REVERT: D 188 MET cc_start: 0.8796 (ttp) cc_final: 0.8478 (ppp) REVERT: D 889 SER cc_start: 0.8949 (p) cc_final: 0.8499 (p) REVERT: D 900 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8142 (mm-40) REVERT: D 990 ASP cc_start: 0.8159 (p0) cc_final: 0.7605 (p0) REVERT: A 165 TYR cc_start: 0.8762 (t80) cc_final: 0.8521 (t80) REVERT: A 323 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8581 (ptpp) REVERT: B 97 MET cc_start: 0.8311 (mtp) cc_final: 0.7930 (ttm) REVERT: B 306 TRP cc_start: 0.9254 (m-10) cc_final: 0.8801 (m-10) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1069 time to fit residues: 19.4046 Evaluate side-chains 93 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 9.9990 chunk 130 optimal weight: 0.0470 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 884 ASN ** C 906 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 941 GLN D1016 HIS B 64 ASN B 292 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061341 restraints weight = 48534.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063090 restraints weight = 29869.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064315 restraints weight = 20927.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065175 restraints weight = 16115.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.065730 restraints weight = 13277.935| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13379 Z= 0.115 Angle : 0.576 7.760 18415 Z= 0.297 Chirality : 0.040 0.157 2120 Planarity : 0.003 0.036 2153 Dihedral : 18.552 75.021 2313 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.23), residues: 1464 helix: 0.60 (0.23), residues: 512 sheet: -1.60 (0.32), residues: 251 loop : -0.88 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.020 0.001 TYR A 316 PHE 0.010 0.001 PHE C 986 TRP 0.012 0.001 TRP C 880 HIS 0.007 0.001 HIS C1016 Details of bonding type rmsd covalent geometry : bond 0.00250 (13379) covalent geometry : angle 0.57611 (18415) hydrogen bonds : bond 0.03068 ( 469) hydrogen bonds : angle 4.40581 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.19 seconds wall clock time: 33 minutes 22.38 seconds (2002.38 seconds total)