Starting phenix.real_space_refine on Sat Sep 12 14:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s85_10116/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.cif" model { file = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s85_10116/09_2026/6s85_10116.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.75, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 561.7 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: 1.49 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: 2.21 Time building geometry restraints manager: 1.39 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=" C3' DA F 50 " pdb=" C2' DA F 50 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+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=" O3' DT F 69 " pdb=" P DG F 70 " ideal model delta sigma weight residual 1.607 1.647 -0.040 1.20e-02 6.94e+03 1.13e+01 ... (remaining 13374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 18191 3.39 - 6.78: 204 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=" O4' DG F 59 " pdb=" C4' DG F 59 " pdb=" C3' DG F 59 " ideal model delta sigma weight residual 106.00 102.24 3.76 6.00e-01 2.78e+00 3.92e+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: 1872 0.094 - 0.189: 232 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- 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= 0.519 Angle : 1.038 16.962 18415 Z= 0.695 Chirality : 0.061 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/Z covalent geometry : bond 0.00803 / 0.52 (13379) covalent geometry : angle 1.03825 / 0.69 (18415) hydrogen bonds : bond 0.21011 / 13.41 ( 469) hydrogen bonds : angle 8.42770 / 5.72 ( 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 : 0.484 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: 0.1360 time to fit residues: 36.3058 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: 30.0000 overall best weight: 0.8332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 184 GLN C 906 ASN C 909 HIS C 914 GLN C 941 GLN C1005 ASN D 10 ASN D 900 GLN A 36 GLN A 277 GLN B 71 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.079178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064076 restraints weight = 47595.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065753 restraints weight = 29990.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.066924 restraints weight = 21350.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067739 restraints weight = 16616.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068312 restraints weight = 13841.075| |-----------------------------------------------------------------------------| 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) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13379 Z= 0.153 Angle : 0.720 8.544 18415 Z= 0.381 Chirality : 0.047 0.249 2120 Planarity : 0.005 0.046 2153 Dihedral : 19.871 91.108 2313 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.08 % Allowed : 4.18 % Favored : 95.74 % 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: -2.61 (0.21), residues: 1464 helix: -1.44 (0.21), residues: 498 sheet: -2.15 (0.29), residues: 268 loop : -1.65 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 382 TYR 0.016 0.002 TYR B 63 PHE 0.017 0.002 PHE C 986 TRP 0.012 0.001 TRP D 96 HIS 0.007 0.001 HIS C 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (13379) covalent geometry : angle 0.72037 / 0.38 (18415) hydrogen bonds : bond 0.05354 / 3.70 ( 469) hydrogen bonds : angle 5.57573 / 3.78 ( 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 173 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 ARG cc_start: 0.8869 (mpp80) cc_final: 0.8393 (mpp80) REVERT: C 197 ARG cc_start: 0.8518 (mmt180) cc_final: 0.7565 (mmp-170) REVERT: C 1036 LEU cc_start: 0.8295 (mm) cc_final: 0.8062 (tp) REVERT: D 11 LEU cc_start: 0.9166 (mm) cc_final: 0.8871 (mm) REVERT: D 188 MET cc_start: 0.8593 (ttp) cc_final: 0.8054 (tmm) REVERT: D 889 SER cc_start: 0.8345 (p) cc_final: 0.7711 (m) REVERT: D 900 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8007 (mm-40) REVERT: D 932 LEU cc_start: 0.9361 (mt) cc_final: 0.9055 (mm) REVERT: D 990 ASP cc_start: 0.8030 (p0) cc_final: 0.7425 (p0) REVERT: A 254 TYR cc_start: 0.8591 (m-80) cc_final: 0.8219 (m-10) REVERT: B 170 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8122 (mmtm) REVERT: B 217 TYR cc_start: 0.8762 (t80) cc_final: 0.8499 (t80) REVERT: B 292 GLN cc_start: 0.8534 (mt0) cc_final: 0.8312 (mt0) REVERT: B 363 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8283 (tm-30) REVERT: B 366 PHE cc_start: 0.9086 (t80) cc_final: 0.8589 (t80) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1189 time to fit residues: 30.1950 Evaluate side-chains 118 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.6980 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 68 GLN C 69 ASN ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 GLN A 38 HIS B 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.077369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062197 restraints weight = 48481.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063856 restraints weight = 30243.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065022 restraints weight = 21454.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065772 restraints weight = 16650.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066380 restraints weight = 13957.006| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13379 Z= 0.134 Angle : 0.644 8.693 18415 Z= 0.340 Chirality : 0.044 0.242 2120 Planarity : 0.004 0.061 2153 Dihedral : 19.689 89.971 2313 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.33 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -2.02 (0.21), residues: 1464 helix: -0.73 (0.22), residues: 502 sheet: -1.95 (0.29), residues: 262 loop : -1.44 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 347 TYR 0.023 0.002 TYR C 92 PHE 0.038 0.001 PHE A 366 TRP 0.007 0.001 TRP C 880 HIS 0.005 0.001 HIS D1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (13379) covalent geometry : angle 0.64417 / 0.34 (18415) hydrogen bonds : bond 0.04646 / 3.16 ( 469) hydrogen bonds : angle 5.12750 / 3.49 ( 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 166 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.8313 (tt0) cc_final: 0.8090 (tt0) REVERT: C 197 ARG cc_start: 0.8537 (mmt180) cc_final: 0.7581 (mmp-170) REVERT: D 188 MET cc_start: 0.8593 (ttp) cc_final: 0.8106 (tmm) REVERT: D 889 SER cc_start: 0.8473 (p) cc_final: 0.7652 (m) REVERT: D 990 ASP cc_start: 0.7880 (p0) cc_final: 0.7274 (p0) REVERT: A 254 TYR cc_start: 0.8532 (m-80) cc_final: 0.8103 (m-10) REVERT: A 323 LYS cc_start: 0.9319 (mtmm) cc_final: 0.9067 (mtmm) REVERT: B 170 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8295 (mmtm) REVERT: B 180 ILE cc_start: 0.9511 (pt) cc_final: 0.9303 (mp) REVERT: B 217 TYR cc_start: 0.8661 (t80) cc_final: 0.8281 (t80) REVERT: B 306 TRP cc_start: 0.9237 (m-10) cc_final: 0.8745 (m-10) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1107 time to fit residues: 27.5788 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 : 0.483 ------------------------------------------------------------------------------- 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: 0.4980 chunk 151 optimal weight: 30.0000 chunk 78 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN C 184 GLN ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 193 HIS A 152 HIS A 318 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.061830 restraints weight = 48990.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063564 restraints weight = 30122.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064784 restraints weight = 21105.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065635 restraints weight = 16262.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066176 restraints weight = 13450.353| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13379 Z= 0.144 Angle : 0.627 7.774 18415 Z= 0.331 Chirality : 0.043 0.226 2120 Planarity : 0.004 0.048 2153 Dihedral : 19.525 88.572 2313 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -1.74 (0.22), residues: 1464 helix: -0.40 (0.22), residues: 507 sheet: -1.85 (0.30), residues: 263 loop : -1.34 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.014 0.001 TYR D 92 PHE 0.017 0.001 PHE B 246 TRP 0.006 0.001 TRP C 880 HIS 0.008 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13379) covalent geometry : angle 0.62659 / 0.33 (18415) hydrogen bonds : bond 0.04391 / 2.99 ( 469) hydrogen bonds : angle 4.84222 / 3.29 ( 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 143 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.8357 (tt0) cc_final: 0.8115 (tt0) REVERT: C 197 ARG cc_start: 0.8490 (mmt180) cc_final: 0.7475 (mmp-170) REVERT: D 188 MET cc_start: 0.8716 (ttp) cc_final: 0.8502 (ppp) REVERT: D 889 SER cc_start: 0.8429 (p) cc_final: 0.7506 (m) REVERT: D 990 ASP cc_start: 0.7919 (p0) cc_final: 0.7398 (p0) REVERT: A 254 TYR cc_start: 0.8700 (m-80) cc_final: 0.8255 (m-10) REVERT: A 322 ARG cc_start: 0.8782 (tpp-160) cc_final: 0.8572 (tpp-160) REVERT: A 323 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8885 (mtmm) REVERT: B 170 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8338 (mmtm) REVERT: B 217 TYR cc_start: 0.8839 (t80) cc_final: 0.8529 (t80) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1031 time to fit residues: 22.3339 Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 909 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS A 227 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060680 restraints weight = 49071.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062490 restraints weight = 29440.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063758 restraints weight = 20321.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.064547 restraints weight = 15492.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065233 restraints weight = 12818.234| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13379 Z= 0.176 Angle : 0.639 7.295 18415 Z= 0.335 Chirality : 0.044 0.213 2120 Planarity : 0.004 0.039 2153 Dihedral : 19.382 86.996 2313 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -1.53 (0.22), residues: 1464 helix: -0.18 (0.23), residues: 508 sheet: -1.82 (0.30), residues: 265 loop : -1.22 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 347 TYR 0.017 0.002 TYR C 92 PHE 0.017 0.001 PHE A 27 TRP 0.007 0.001 TRP D 940 HIS 0.007 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (13379) covalent geometry : angle 0.63940 / 0.34 (18415) hydrogen bonds : bond 0.04384 / 3.00 ( 469) hydrogen bonds : angle 4.77591 / 3.24 ( 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 133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 GLN cc_start: 0.8373 (tt0) cc_final: 0.8117 (tt0) REVERT: C 197 ARG cc_start: 0.8469 (mmt180) cc_final: 0.7512 (mmp-170) REVERT: C 1038 TYR cc_start: 0.8336 (m-10) cc_final: 0.8133 (m-80) REVERT: D 11 LEU cc_start: 0.9216 (mm) cc_final: 0.8997 (mm) REVERT: D 175 GLU cc_start: 0.7692 (mp0) cc_final: 0.7265 (mp0) REVERT: D 889 SER cc_start: 0.8498 (p) cc_final: 0.7508 (m) REVERT: D 983 ASP cc_start: 0.7914 (t70) cc_final: 0.7615 (t0) REVERT: D 990 ASP cc_start: 0.7896 (p0) cc_final: 0.7402 (p0) REVERT: A 149 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8537 (mmmm) REVERT: A 322 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8452 (tpp-160) REVERT: A 347 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7138 (ttt180) REVERT: B 170 LYS cc_start: 0.8612 (mmtt) cc_final: 0.8186 (mmtm) REVERT: B 246 PHE cc_start: 0.8394 (m-80) cc_final: 0.8130 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1051 time to fit residues: 21.0621 Evaluate side-chains 104 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 9.9990 chunk 142 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 GLN A 36 GLN A 110 HIS B 76 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.058041 restraints weight = 50369.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059671 restraints weight = 31592.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.060841 restraints weight = 22466.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061651 restraints weight = 17469.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062231 restraints weight = 14546.142| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 13379 Z= 0.312 Angle : 0.786 10.842 18415 Z= 0.404 Chirality : 0.047 0.220 2120 Planarity : 0.005 0.053 2153 Dihedral : 19.417 85.623 2313 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.96 % Rotamer: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % 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: -1.74 (0.22), residues: 1464 helix: -0.29 (0.22), residues: 508 sheet: -2.06 (0.31), residues: 248 loop : -1.37 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 896 TYR 0.024 0.003 TYR C 92 PHE 0.023 0.002 PHE C 898 TRP 0.021 0.002 TRP D 940 HIS 0.009 0.002 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.31 (13379) covalent geometry : angle 0.78560 / 0.40 (18415) hydrogen bonds : bond 0.05719 / 3.98 ( 469) hydrogen bonds : angle 5.13493 / 3.45 ( 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 120 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 ARG cc_start: 0.8736 (mmt90) cc_final: 0.8395 (mmm160) REVERT: C 1038 TYR cc_start: 0.8472 (m-10) cc_final: 0.8267 (m-80) REVERT: D 175 GLU cc_start: 0.8124 (mp0) cc_final: 0.7880 (mp0) REVERT: D 188 MET cc_start: 0.8532 (ppp) cc_final: 0.8325 (ppp) REVERT: D 889 SER cc_start: 0.8441 (p) cc_final: 0.8055 (p) REVERT: D 900 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8256 (mm-40) REVERT: D 990 ASP cc_start: 0.8109 (p0) cc_final: 0.7545 (p0) REVERT: A 308 ASP cc_start: 0.8925 (t70) cc_final: 0.8711 (t70) REVERT: A 322 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.8284 (tpp-160) REVERT: A 347 ARG cc_start: 0.7541 (ttt180) cc_final: 0.7328 (ttt180) REVERT: B 170 LYS cc_start: 0.8873 (mmpt) cc_final: 0.8526 (mmtm) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1060 time to fit residues: 19.4972 Evaluate side-chains 88 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 9.9990 chunk 141 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.075580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060129 restraints weight = 48931.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.061813 restraints weight = 30444.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.063006 restraints weight = 21512.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063828 restraints weight = 16670.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064389 restraints weight = 13851.373| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13379 Z= 0.153 Angle : 0.643 8.089 18415 Z= 0.336 Chirality : 0.044 0.227 2120 Planarity : 0.004 0.035 2153 Dihedral : 19.300 88.914 2313 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: -1.47 (0.22), residues: 1464 helix: -0.11 (0.23), residues: 509 sheet: -1.88 (0.32), residues: 244 loop : -1.20 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 149 TYR 0.015 0.001 TYR D 92 PHE 0.029 0.002 PHE A 366 TRP 0.010 0.001 TRP D 18 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (13379) covalent geometry : angle 0.64302 / 0.34 (18415) hydrogen bonds : bond 0.04284 / 2.89 ( 469) hydrogen bonds : angle 4.83752 / 3.27 ( 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 131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.491 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 149 ARG cc_start: 0.8680 (mmt90) cc_final: 0.8431 (mmm160) REVERT: C 1038 TYR cc_start: 0.8407 (m-10) cc_final: 0.8198 (m-80) REVERT: D 889 SER cc_start: 0.8494 (p) cc_final: 0.8134 (p) REVERT: D 983 ASP cc_start: 0.7521 (t70) cc_final: 0.7232 (t0) REVERT: D 990 ASP cc_start: 0.8008 (p0) cc_final: 0.7458 (p0) REVERT: A 149 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8502 (mmmm) REVERT: A 308 ASP cc_start: 0.9038 (t70) cc_final: 0.8772 (t70) REVERT: A 322 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8230 (tpp-160) REVERT: A 323 LYS cc_start: 0.9269 (mtmm) cc_final: 0.8916 (mtmm) REVERT: B 97 MET cc_start: 0.8479 (mtp) cc_final: 0.8030 (mtp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1143 time to fit residues: 22.3511 Evaluate side-chains 105 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 0.7980 chunk 85 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.061711 restraints weight = 48569.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063436 restraints weight = 29841.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.064657 restraints weight = 20942.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065513 restraints weight = 16125.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066119 restraints weight = 13321.287| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13379 Z= 0.115 Angle : 0.617 8.997 18415 Z= 0.319 Chirality : 0.043 0.213 2120 Planarity : 0.003 0.033 2153 Dihedral : 19.088 88.073 2313 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.60 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.29 (0.22), residues: 1464 helix: 0.06 (0.23), residues: 501 sheet: -1.62 (0.32), residues: 253 loop : -1.15 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 896 TYR 0.035 0.002 TYR C 92 PHE 0.016 0.001 PHE A 27 TRP 0.011 0.001 TRP C 880 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (13379) covalent geometry : angle 0.61676 / 0.32 (18415) hydrogen bonds : bond 0.03815 / 2.52 ( 469) hydrogen bonds : angle 4.65663 / 3.16 ( 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 140 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 ARG cc_start: 0.8632 (mmt90) cc_final: 0.8400 (mmm160) REVERT: C 197 ARG cc_start: 0.8454 (mmt180) cc_final: 0.7520 (mmp-170) REVERT: D 889 SER cc_start: 0.8383 (p) cc_final: 0.8062 (p) REVERT: D 990 ASP cc_start: 0.7893 (p0) cc_final: 0.7347 (p0) REVERT: A 149 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8418 (mmmm) REVERT: A 308 ASP cc_start: 0.9032 (t70) cc_final: 0.8787 (t70) REVERT: A 322 ARG cc_start: 0.8714 (tpp-160) cc_final: 0.8464 (tpp-160) REVERT: A 323 LYS cc_start: 0.9253 (mtmm) cc_final: 0.8945 (mtmm) REVERT: A 347 ARG cc_start: 0.7523 (ttt180) cc_final: 0.6933 (ttt180) REVERT: B 97 MET cc_start: 0.8375 (mtp) cc_final: 0.8001 (mtp) REVERT: B 170 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8234 (mmtm) REVERT: B 306 TRP cc_start: 0.9315 (m-10) cc_final: 0.8777 (m-10) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1080 time to fit residues: 22.7874 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 30.0000 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060373 restraints weight = 49227.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062164 restraints weight = 29659.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063394 restraints weight = 20551.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.064260 restraints weight = 15737.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064875 restraints weight = 12932.932| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 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 = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13379 Z= 0.164 Angle : 0.627 9.932 18415 Z= 0.327 Chirality : 0.043 0.215 2120 Planarity : 0.003 0.033 2153 Dihedral : 19.057 85.614 2313 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.26 (0.22), residues: 1464 helix: 0.11 (0.23), residues: 506 sheet: -1.66 (0.32), residues: 255 loop : -1.14 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 896 TYR 0.023 0.002 TYR B 63 PHE 0.017 0.001 PHE A 27 TRP 0.010 0.001 TRP D 940 HIS 0.006 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (13379) covalent geometry : angle 0.62735 / 0.33 (18415) hydrogen bonds : bond 0.04079 / 2.73 ( 469) hydrogen bonds : angle 4.70225 / 3.17 ( 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 138 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 ARG cc_start: 0.8637 (mmt90) cc_final: 0.8396 (mmm160) REVERT: C 197 ARG cc_start: 0.8434 (mmt180) cc_final: 0.7514 (mmp-170) REVERT: D 889 SER cc_start: 0.8432 (p) cc_final: 0.8094 (p) REVERT: D 990 ASP cc_start: 0.7945 (p0) cc_final: 0.7451 (p0) REVERT: A 308 ASP cc_start: 0.9048 (t70) cc_final: 0.8839 (t70) REVERT: A 322 ARG cc_start: 0.8710 (tpp-160) cc_final: 0.8208 (tpp-160) REVERT: B 97 MET cc_start: 0.8453 (mtp) cc_final: 0.8042 (mtp) REVERT: B 170 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8130 (mmtm) REVERT: B 306 TRP cc_start: 0.9313 (m-10) cc_final: 0.8752 (m-10) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1152 time to fit residues: 23.7672 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 : 0.521 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.076572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060963 restraints weight = 48974.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062755 restraints weight = 29562.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.063993 restraints weight = 20528.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064886 restraints weight = 15773.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065409 restraints weight = 12922.303| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13379 Z= 0.129 Angle : 0.610 12.086 18415 Z= 0.316 Chirality : 0.043 0.221 2120 Planarity : 0.003 0.032 2153 Dihedral : 18.988 84.745 2313 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -1.17 (0.22), residues: 1464 helix: 0.17 (0.23), residues: 508 sheet: -1.58 (0.32), residues: 255 loop : -1.08 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 896 TYR 0.023 0.001 TYR B 63 PHE 0.016 0.001 PHE A 27 TRP 0.010 0.001 TRP C 880 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (13379) covalent geometry : angle 0.60964 / 0.32 (18415) hydrogen bonds : bond 0.03739 / 2.45 ( 469) hydrogen bonds : angle 4.63913 / 3.14 ( 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 135 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 889 SER cc_start: 0.8475 (p) cc_final: 0.8154 (p) REVERT: D 990 ASP cc_start: 0.7896 (p0) cc_final: 0.7396 (p0) REVERT: A 322 ARG cc_start: 0.8696 (tpp-160) cc_final: 0.8217 (tpp-160) REVERT: A 323 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8802 (mtmm) REVERT: B 97 MET cc_start: 0.8410 (mtp) cc_final: 0.7995 (mtp) REVERT: B 170 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8101 (mmtm) REVERT: B 306 TRP cc_start: 0.9295 (m-10) cc_final: 0.8754 (m-10) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1073 time to fit residues: 22.1795 Evaluate side-chains 101 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 4.9990 chunk 41 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 941 GLN A 256 HIS ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.076756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.061309 restraints weight = 48633.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063097 restraints weight = 29294.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064345 restraints weight = 20300.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.065191 restraints weight = 15487.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065819 restraints weight = 12724.819| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3422 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 : 0.607 8.411 18415 Z= 0.315 Chirality : 0.043 0.217 2120 Planarity : 0.003 0.071 2153 Dihedral : 18.949 83.009 2313 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.13 (0.22), residues: 1464 helix: 0.16 (0.23), residues: 514 sheet: -1.56 (0.32), residues: 255 loop : -1.03 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 149 TYR 0.027 0.002 TYR C1038 PHE 0.016 0.001 PHE A 27 TRP 0.009 0.001 TRP C 880 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (13379) covalent geometry : angle 0.60733 / 0.31 (18415) hydrogen bonds : bond 0.03711 / 2.44 ( 469) hydrogen bonds : angle 4.61131 / 3.12 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.20 seconds wall clock time: 34 minutes 23.32 seconds (2063.32 seconds total)