Starting phenix.real_space_refine on Thu Mar 5 03:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl0_27494/03_2026/8dl0_27494.cif" } resolution = 4.1 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= 0.002 sd= 0.041 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 10294 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6922 2.51 5 N 1627 2.21 5 O 1796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10377 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3078 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain breaks: 1 Chain: "B" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2126 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "C" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3047 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 12, 'TRANS': 365} Chain breaks: 1 Chain: "D" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2126 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Time building chain proxies: 2.31, per 1000 atoms: 0.22 Number of scatterers: 10377 At special positions: 0 Unit cell: (96.12, 87.48, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1796 8.00 N 1627 7.00 C 6922 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: 0.66 Conformation dependent library (CDL) restraints added in 509.9 milliseconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.9% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.780A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.536A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.621A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 3.744A pdb=" N ASN A 136 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.675A pdb=" N ALA A 170 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 190 removed outlier: 3.633A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.580A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 88 Proline residue: B 70 - end of helix removed outlier: 3.722A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 100 through 129 removed outlier: 3.552A pdb=" N VAL B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.998A pdb=" N TYR B 136 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TYR B 138 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 165 removed outlier: 4.333A pdb=" N ALA B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 181 removed outlier: 3.519A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.618A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.585A pdb=" N VAL B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.589A pdb=" N LEU B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 5.052A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 4.294A pdb=" N ILE C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.938A pdb=" N THR C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 114 through 130 removed outlier: 4.764A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.860A pdb=" N ASN C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.509A pdb=" N ILE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 189 Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 224 through 237 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 54 through 84 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 84 through 93 removed outlier: 3.976A pdb=" N LYS D 89 " --> pdb=" O PHE D 85 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 129 removed outlier: 3.822A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 removed outlier: 3.611A pdb=" N LYS D 135 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 136 " --> pdb=" O GLY D 133 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR D 138 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 164 removed outlier: 4.280A pdb=" N LEU D 144 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 removed outlier: 3.677A pdb=" N ILE D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.876A pdb=" N ILE D 191 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 202 removed outlier: 3.843A pdb=" N TYR D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 removed outlier: 4.238A pdb=" N VAL D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 255 Proline residue: D 235 - end of helix removed outlier: 4.843A pdb=" N LYS D 250 " --> pdb=" O LYS D 246 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 43 removed outlier: 5.677A pdb=" N GLU A 33 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N TRP A 35 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR A 11 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 7 " --> pdb=" O GLY A 39 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN A 41 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE A 5 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 43 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A 3 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.198A pdb=" N VAL A 85 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 211 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU A 222 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 213 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 220 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 265 removed outlier: 6.486A pdb=" N ASP A 285 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 262 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU A 283 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 264 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE A 281 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 326 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS A 327 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 394 " --> pdb=" O LYS A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 276 removed outlier: 6.352A pdb=" N PHE A 274 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY A 373 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS A 359 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 351 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 347 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 365 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 345 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N CYS A 367 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR A 343 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE A 369 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N GLY A 341 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 310 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP A 303 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASP A 308 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 394 removed outlier: 4.276A pdb=" N LYS C 327 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 261 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLU C 287 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 259 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 43 removed outlier: 5.409A pdb=" N GLU C 33 " --> pdb=" O TYR C 13 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR C 13 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TRP C 35 " --> pdb=" O TYR C 11 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N TYR C 11 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL C 7 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN C 41 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE C 5 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLU C 43 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ARG C 3 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 5 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 77 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 7 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 75 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.261A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA C 211 " --> pdb=" O GLU C 222 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU C 222 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU C 213 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 276 removed outlier: 6.340A pdb=" N PHE C 274 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY C 373 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N CYS C 359 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS C 351 " --> pdb=" O CYS C 359 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 347 " --> pdb=" O ILE C 363 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 365 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU C 345 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 367 " --> pdb=" O TYR C 343 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR C 343 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE C 369 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY C 341 " --> pdb=" O PHE C 369 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3107 1.34 - 1.46: 2420 1.46 - 1.58: 5070 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 10649 Sorted by residual: bond pdb=" N GLU C 358 " pdb=" CA GLU C 358 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.46e+00 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.49e+00 bond pdb=" N ASN A 390 " pdb=" CA ASN A 390 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.13e+00 bond pdb=" N MET C 317 " pdb=" CA MET C 317 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.33e-02 5.65e+03 4.73e+00 bond pdb=" N CYS C 359 " pdb=" CA CYS C 359 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.46e-02 4.69e+03 4.34e+00 ... (remaining 10644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 13979 1.64 - 3.27: 335 3.27 - 4.91: 57 4.91 - 6.55: 23 6.55 - 8.18: 8 Bond angle restraints: 14402 Sorted by residual: angle pdb=" N LEU C 316 " pdb=" CA LEU C 316 " pdb=" C LEU C 316 " ideal model delta sigma weight residual 113.01 106.53 6.48 1.20e+00 6.94e-01 2.92e+01 angle pdb=" N ILE A 394 " pdb=" CA ILE A 394 " pdb=" C ILE A 394 " ideal model delta sigma weight residual 107.61 113.83 -6.22 1.19e+00 7.06e-01 2.73e+01 angle pdb=" N ILE A 394 " pdb=" CA ILE A 394 " pdb=" CB ILE A 394 " ideal model delta sigma weight residual 112.37 106.87 5.50 1.06e+00 8.90e-01 2.69e+01 angle pdb=" N GLU D 13 " pdb=" CA GLU D 13 " pdb=" CB GLU D 13 " ideal model delta sigma weight residual 110.16 116.62 -6.46 1.48e+00 4.57e-01 1.91e+01 angle pdb=" C GLU C 358 " pdb=" CA GLU C 358 " pdb=" CB GLU C 358 " ideal model delta sigma weight residual 110.42 102.24 8.18 1.99e+00 2.53e-01 1.69e+01 ... (remaining 14397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5694 17.73 - 35.47: 461 35.47 - 53.20: 65 53.20 - 70.93: 11 70.93 - 88.66: 9 Dihedral angle restraints: 6240 sinusoidal: 2544 harmonic: 3696 Sorted by residual: dihedral pdb=" C GLU C 358 " pdb=" N GLU C 358 " pdb=" CA GLU C 358 " pdb=" CB GLU C 358 " ideal model delta harmonic sigma weight residual -122.60 -112.57 -10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" C LYS A 393 " pdb=" N LYS A 393 " pdb=" CA LYS A 393 " pdb=" CB LYS A 393 " ideal model delta harmonic sigma weight residual -122.60 -113.45 -9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N GLY B 52 " pdb=" CA GLY B 52 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 6237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1387 0.064 - 0.127: 209 0.127 - 0.191: 15 0.191 - 0.254: 3 0.254 - 0.318: 1 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CA GLU C 358 " pdb=" N GLU C 358 " pdb=" C GLU C 358 " pdb=" CB GLU C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA MET C 317 " pdb=" N MET C 317 " pdb=" C MET C 317 " pdb=" CB MET C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS A 393 " pdb=" N LYS A 393 " pdb=" C LYS A 393 " pdb=" CB LYS A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1612 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 9 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C LEU D 9 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL D 10 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 244 " 0.013 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE B 244 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 244 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 244 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 244 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 244 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 244 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 358 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.15e+00 pdb=" C GLU C 358 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU C 358 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS C 359 " 0.011 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 376 2.71 - 3.26: 10942 3.26 - 3.81: 17269 3.81 - 4.35: 20621 4.35 - 4.90: 34237 Nonbonded interactions: 83445 Sorted by model distance: nonbonded pdb=" NH1 ARG A 392 " pdb=" O LYS A 393 " model vdw 2.168 3.120 nonbonded pdb=" OG1 THR D 188 " pdb=" OH TYR D 219 " model vdw 2.221 3.040 nonbonded pdb=" O LEU D 192 " pdb=" NZ LYS D 197 " model vdw 2.222 3.120 nonbonded pdb=" O GLY D 83 " pdb=" OG1 THR D 86 " model vdw 2.236 3.040 nonbonded pdb=" O PRO A 138 " pdb=" OG1 THR A 141 " model vdw 2.240 3.040 ... (remaining 83440 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 2 through 237 or resid 254 through 395)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.710 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 : 0.003 0.040 10649 Z= 0.149 Angle : 0.668 8.185 14402 Z= 0.385 Chirality : 0.045 0.318 1615 Planarity : 0.003 0.032 1768 Dihedral : 13.217 88.664 3872 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.25 (0.24), residues: 1256 helix: 1.31 (0.22), residues: 579 sheet: 1.13 (0.39), residues: 176 loop : -1.62 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 166 TYR 0.014 0.001 TYR D 18 PHE 0.032 0.001 PHE B 244 TRP 0.014 0.001 TRP D 26 HIS 0.007 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00269 (10649) covalent geometry : angle 0.66752 (14402) hydrogen bonds : bond 0.16373 ( 526) hydrogen bonds : angle 6.98919 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8033 (m90) cc_final: 0.7515 (m90) REVERT: A 178 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8014 (tp40) REVERT: B 53 HIS cc_start: 0.8245 (m-70) cc_final: 0.7973 (m-70) REVERT: B 76 ASN cc_start: 0.8180 (t0) cc_final: 0.7796 (t0) REVERT: B 89 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9091 (tttt) REVERT: B 93 THR cc_start: 0.9132 (p) cc_final: 0.8922 (p) REVERT: B 110 GLU cc_start: 0.8402 (tp30) cc_final: 0.8160 (tp30) REVERT: B 113 ASN cc_start: 0.8539 (p0) cc_final: 0.8276 (p0) REVERT: B 169 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8672 (tptp) REVERT: B 206 TYR cc_start: 0.8138 (t80) cc_final: 0.7860 (t80) REVERT: B 219 TYR cc_start: 0.7320 (t80) cc_final: 0.6714 (t80) REVERT: B 236 LEU cc_start: 0.9107 (tp) cc_final: 0.8869 (tp) REVERT: C 98 LEU cc_start: 0.8571 (mm) cc_final: 0.8320 (mm) REVERT: C 334 MET cc_start: 0.6262 (tpt) cc_final: 0.6030 (tpt) REVERT: D 80 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8323 (ttp-170) REVERT: D 88 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8704 (mmmt) REVERT: D 91 LEU cc_start: 0.9214 (mt) cc_final: 0.8894 (mt) REVERT: D 205 MET cc_start: 0.8759 (mmm) cc_final: 0.8445 (mmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0759 time to fit residues: 21.5811 Evaluate side-chains 136 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 390 ASN B 213 HIS C 175 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.076162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065274 restraints weight = 57781.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066846 restraints weight = 38652.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067983 restraints weight = 28524.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068868 restraints weight = 22434.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.069488 restraints weight = 18493.019| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10649 Z= 0.214 Angle : 0.654 7.423 14402 Z= 0.348 Chirality : 0.044 0.148 1615 Planarity : 0.004 0.054 1768 Dihedral : 4.967 19.399 1364 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.18 % Allowed : 4.92 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.24), residues: 1256 helix: 0.87 (0.21), residues: 592 sheet: 1.02 (0.38), residues: 186 loop : -1.49 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 166 TYR 0.020 0.002 TYR D 138 PHE 0.024 0.002 PHE D 179 TRP 0.020 0.002 TRP C 362 HIS 0.009 0.002 HIS D 213 Details of bonding type rmsd covalent geometry : bond 0.00461 (10649) covalent geometry : angle 0.65419 (14402) hydrogen bonds : bond 0.04778 ( 526) hydrogen bonds : angle 5.74867 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.353 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: A 140 LYS cc_start: 0.9172 (ptpp) cc_final: 0.8896 (pttm) REVERT: A 178 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8260 (tp40) REVERT: B 76 ASN cc_start: 0.8548 (t0) cc_final: 0.8130 (t0) REVERT: B 110 GLU cc_start: 0.8518 (tp30) cc_final: 0.8275 (tp30) REVERT: B 169 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8787 (tptp) REVERT: B 219 TYR cc_start: 0.7424 (t80) cc_final: 0.6877 (t80) REVERT: C 95 ASN cc_start: 0.9102 (t0) cc_final: 0.8768 (t0) REVERT: C 98 LEU cc_start: 0.8568 (mm) cc_final: 0.8037 (mm) REVERT: C 178 GLN cc_start: 0.9029 (pt0) cc_final: 0.8557 (pp30) REVERT: C 334 MET cc_start: 0.6547 (tpt) cc_final: 0.6277 (tpt) REVERT: D 80 ARG cc_start: 0.8652 (tmm-80) cc_final: 0.8056 (ttp-170) REVERT: D 88 LYS cc_start: 0.9518 (mmmt) cc_final: 0.9313 (mmmt) REVERT: D 249 GLU cc_start: 0.8717 (pt0) cc_final: 0.8383 (pt0) outliers start: 2 outliers final: 0 residues processed: 169 average time/residue: 0.0882 time to fit residues: 21.7449 Evaluate side-chains 118 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.0270 chunk 113 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 124 optimal weight: 0.0170 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN ** D 223 HIS ** 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 = 0.3646 r_free = 0.3646 target = 0.078307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.067151 restraints weight = 56991.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.068752 restraints weight = 37971.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069865 restraints weight = 27957.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.070717 restraints weight = 22170.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.071347 restraints weight = 18336.387| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10649 Z= 0.112 Angle : 0.545 7.386 14402 Z= 0.287 Chirality : 0.042 0.136 1615 Planarity : 0.004 0.047 1768 Dihedral : 4.569 18.365 1364 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.26 (0.24), residues: 1256 helix: 1.11 (0.22), residues: 594 sheet: 1.45 (0.39), residues: 174 loop : -1.53 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 166 TYR 0.013 0.001 TYR D 138 PHE 0.027 0.001 PHE A 152 TRP 0.017 0.001 TRP D 26 HIS 0.008 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00232 (10649) covalent geometry : angle 0.54467 (14402) hydrogen bonds : bond 0.04106 ( 526) hydrogen bonds : angle 5.23783 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8335 (m90) cc_final: 0.7849 (m90) REVERT: A 178 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8155 (tp40) REVERT: B 76 ASN cc_start: 0.8554 (t0) cc_final: 0.8155 (t0) REVERT: B 110 GLU cc_start: 0.8360 (tp30) cc_final: 0.8149 (tp30) REVERT: B 114 TYR cc_start: 0.8251 (t80) cc_final: 0.7353 (t80) REVERT: B 206 TYR cc_start: 0.8087 (t80) cc_final: 0.7814 (t80) REVERT: B 219 TYR cc_start: 0.7454 (t80) cc_final: 0.6849 (t80) REVERT: B 252 ILE cc_start: 0.9478 (pt) cc_final: 0.9275 (mt) REVERT: C 95 ASN cc_start: 0.9076 (t0) cc_final: 0.8689 (t0) REVERT: C 98 LEU cc_start: 0.8562 (mm) cc_final: 0.7980 (mm) REVERT: C 178 GLN cc_start: 0.8926 (pt0) cc_final: 0.8490 (pp30) REVERT: C 334 MET cc_start: 0.6491 (tpt) cc_final: 0.6275 (tpt) REVERT: D 80 ARG cc_start: 0.8730 (tmm-80) cc_final: 0.7946 (ttp-170) REVERT: D 249 GLU cc_start: 0.8555 (pt0) cc_final: 0.8304 (pt0) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0826 time to fit residues: 22.4909 Evaluate side-chains 130 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 107 ASN A 378 GLN C 175 HIS D 76 ASN ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.073649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.062939 restraints weight = 60140.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064481 restraints weight = 39745.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065617 restraints weight = 29021.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066451 restraints weight = 22706.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.067070 restraints weight = 18673.449| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10649 Z= 0.288 Angle : 0.751 8.684 14402 Z= 0.396 Chirality : 0.047 0.170 1615 Planarity : 0.005 0.073 1768 Dihedral : 5.454 21.209 1364 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1256 helix: 0.45 (0.21), residues: 590 sheet: 0.74 (0.38), residues: 187 loop : -1.49 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 166 TYR 0.025 0.002 TYR D 138 PHE 0.031 0.003 PHE B 137 TRP 0.017 0.002 TRP D 26 HIS 0.009 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00619 (10649) covalent geometry : angle 0.75100 (14402) hydrogen bonds : bond 0.05022 ( 526) hydrogen bonds : angle 5.81715 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8369 (m90) cc_final: 0.7914 (m90) REVERT: B 76 ASN cc_start: 0.8587 (t0) cc_final: 0.8205 (t0) REVERT: B 88 LYS cc_start: 0.9532 (mppt) cc_final: 0.9324 (mptt) REVERT: B 110 GLU cc_start: 0.8602 (tp30) cc_final: 0.8262 (tp30) REVERT: B 113 ASN cc_start: 0.8517 (p0) cc_final: 0.8288 (p0) REVERT: B 206 TYR cc_start: 0.8357 (t80) cc_final: 0.7905 (t80) REVERT: C 178 GLN cc_start: 0.9010 (pt0) cc_final: 0.8641 (pp30) REVERT: C 334 MET cc_start: 0.6887 (tpt) cc_final: 0.6632 (tpt) REVERT: D 71 TRP cc_start: 0.8224 (t60) cc_final: 0.7900 (t60) REVERT: D 88 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9415 (mmmt) REVERT: D 249 GLU cc_start: 0.8736 (pt0) cc_final: 0.8425 (pt0) outliers start: 2 outliers final: 0 residues processed: 137 average time/residue: 0.0785 time to fit residues: 16.2292 Evaluate side-chains 102 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN C 268 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.064864 restraints weight = 57876.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.066524 restraints weight = 38142.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.067683 restraints weight = 27776.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068557 restraints weight = 21677.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069167 restraints weight = 17774.488| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10649 Z= 0.121 Angle : 0.586 8.545 14402 Z= 0.306 Chirality : 0.043 0.203 1615 Planarity : 0.004 0.058 1768 Dihedral : 4.886 19.113 1364 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.09 % Allowed : 1.76 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.24), residues: 1256 helix: 0.78 (0.21), residues: 594 sheet: 1.30 (0.42), residues: 161 loop : -1.56 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 166 TYR 0.018 0.001 TYR D 138 PHE 0.025 0.002 PHE A 152 TRP 0.017 0.001 TRP D 26 HIS 0.008 0.001 HIS A 361 Details of bonding type rmsd covalent geometry : bond 0.00256 (10649) covalent geometry : angle 0.58629 (14402) hydrogen bonds : bond 0.04132 ( 526) hydrogen bonds : angle 5.21382 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8282 (m90) cc_final: 0.7978 (m90) REVERT: A 178 GLN cc_start: 0.8709 (tp-100) cc_final: 0.8287 (tp40) REVERT: B 76 ASN cc_start: 0.8555 (t0) cc_final: 0.8132 (t0) REVERT: B 110 GLU cc_start: 0.8526 (tp30) cc_final: 0.8250 (tp30) REVERT: B 249 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7743 (mt-10) REVERT: C 95 ASN cc_start: 0.9130 (t0) cc_final: 0.8755 (t0) REVERT: C 98 LEU cc_start: 0.8592 (mm) cc_final: 0.8017 (mm) REVERT: C 146 MET cc_start: 0.8953 (mtt) cc_final: 0.8752 (mtt) REVERT: C 178 GLN cc_start: 0.9008 (pt0) cc_final: 0.8531 (pp30) REVERT: D 71 TRP cc_start: 0.8186 (t60) cc_final: 0.7869 (t60) REVERT: D 249 GLU cc_start: 0.8690 (pt0) cc_final: 0.8348 (pt0) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.0771 time to fit residues: 19.5920 Evaluate side-chains 115 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065265 restraints weight = 58834.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066866 restraints weight = 38463.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068064 restraints weight = 28286.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.068920 restraints weight = 22007.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.069598 restraints weight = 18197.523| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10649 Z= 0.124 Angle : 0.584 8.822 14402 Z= 0.302 Chirality : 0.043 0.153 1615 Planarity : 0.004 0.046 1768 Dihedral : 4.763 18.611 1364 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1256 helix: 0.79 (0.21), residues: 595 sheet: 1.20 (0.42), residues: 166 loop : -1.49 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 166 TYR 0.017 0.001 TYR D 138 PHE 0.025 0.002 PHE A 152 TRP 0.017 0.001 TRP D 26 HIS 0.008 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00271 (10649) covalent geometry : angle 0.58426 (14402) hydrogen bonds : bond 0.03961 ( 526) hydrogen bonds : angle 5.09559 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8298 (m90) cc_final: 0.7976 (m90) REVERT: A 178 GLN cc_start: 0.8681 (tp-100) cc_final: 0.8265 (tp40) REVERT: B 76 ASN cc_start: 0.8545 (t0) cc_final: 0.8112 (t0) REVERT: B 110 GLU cc_start: 0.8558 (tp30) cc_final: 0.8177 (tp30) REVERT: B 219 TYR cc_start: 0.7437 (t80) cc_final: 0.7068 (t80) REVERT: B 221 ASP cc_start: 0.7562 (p0) cc_final: 0.7072 (p0) REVERT: B 236 LEU cc_start: 0.9091 (tp) cc_final: 0.8856 (tp) REVERT: B 251 ASP cc_start: 0.8268 (p0) cc_final: 0.8064 (t0) REVERT: C 95 ASN cc_start: 0.9131 (t0) cc_final: 0.8746 (t0) REVERT: C 98 LEU cc_start: 0.8544 (mm) cc_final: 0.7971 (mm) REVERT: C 178 GLN cc_start: 0.9007 (pt0) cc_final: 0.8542 (pp30) REVERT: D 80 ARG cc_start: 0.8370 (ttp-170) cc_final: 0.7370 (ttp-170) REVERT: D 249 GLU cc_start: 0.8735 (pt0) cc_final: 0.8442 (pt0) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.0803 time to fit residues: 20.0587 Evaluate side-chains 120 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 199 HIS C 175 HIS ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064384 restraints weight = 58168.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066001 restraints weight = 38267.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067152 restraints weight = 27901.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068013 restraints weight = 21765.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.068657 restraints weight = 17900.934| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10649 Z= 0.163 Angle : 0.622 9.166 14402 Z= 0.323 Chirality : 0.044 0.145 1615 Planarity : 0.004 0.058 1768 Dihedral : 4.895 18.949 1364 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.18 % Allowed : 1.76 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1256 helix: 0.77 (0.21), residues: 587 sheet: 0.86 (0.40), residues: 181 loop : -1.34 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 166 TYR 0.019 0.001 TYR D 138 PHE 0.023 0.002 PHE A 152 TRP 0.018 0.001 TRP D 26 HIS 0.008 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00356 (10649) covalent geometry : angle 0.62165 (14402) hydrogen bonds : bond 0.04215 ( 526) hydrogen bonds : angle 5.21873 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8320 (m90) cc_final: 0.8052 (m90) REVERT: A 178 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8280 (tp40) REVERT: B 76 ASN cc_start: 0.8544 (t0) cc_final: 0.8276 (t0) REVERT: B 212 HIS cc_start: 0.8109 (m90) cc_final: 0.7828 (m90) REVERT: B 219 TYR cc_start: 0.7362 (t80) cc_final: 0.6768 (t80) REVERT: B 236 LEU cc_start: 0.9111 (tp) cc_final: 0.8867 (tp) REVERT: B 249 GLU cc_start: 0.8475 (tt0) cc_final: 0.7901 (mt-10) REVERT: C 95 ASN cc_start: 0.9173 (t0) cc_final: 0.8818 (t0) REVERT: C 98 LEU cc_start: 0.8612 (mm) cc_final: 0.8031 (mm) REVERT: C 149 ARG cc_start: 0.9216 (mpp80) cc_final: 0.8966 (mpp80) REVERT: C 178 GLN cc_start: 0.9047 (pt0) cc_final: 0.8556 (pp30) REVERT: D 80 ARG cc_start: 0.8414 (ttp-170) cc_final: 0.7407 (ttp-170) REVERT: D 88 LYS cc_start: 0.9610 (mmmt) cc_final: 0.8996 (mmmt) REVERT: D 91 LEU cc_start: 0.9275 (mt) cc_final: 0.8997 (mt) REVERT: D 249 GLU cc_start: 0.8731 (pt0) cc_final: 0.8454 (pt0) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.0788 time to fit residues: 19.0800 Evaluate side-chains 121 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 44 optimal weight: 0.0030 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 98 optimal weight: 7.9990 overall best weight: 0.7932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 55 ASN C 175 HIS D 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.077625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.066479 restraints weight = 56917.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068123 restraints weight = 37526.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069290 restraints weight = 27277.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.070191 restraints weight = 21221.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.070862 restraints weight = 17410.271| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10649 Z= 0.112 Angle : 0.591 8.215 14402 Z= 0.301 Chirality : 0.043 0.181 1615 Planarity : 0.004 0.054 1768 Dihedral : 4.631 17.902 1364 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.18 % Allowed : 1.93 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1256 helix: 0.81 (0.21), residues: 603 sheet: 1.27 (0.43), residues: 164 loop : -1.54 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 166 TYR 0.015 0.001 TYR D 138 PHE 0.024 0.001 PHE A 152 TRP 0.018 0.001 TRP D 26 HIS 0.008 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00243 (10649) covalent geometry : angle 0.59145 (14402) hydrogen bonds : bond 0.03815 ( 526) hydrogen bonds : angle 4.99555 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8270 (m90) cc_final: 0.7950 (m90) REVERT: A 178 GLN cc_start: 0.8653 (tp-100) cc_final: 0.8258 (tp40) REVERT: B 76 ASN cc_start: 0.8532 (t0) cc_final: 0.8077 (t0) REVERT: B 89 LYS cc_start: 0.9277 (ptpp) cc_final: 0.8864 (ptpp) REVERT: B 110 GLU cc_start: 0.8345 (tp30) cc_final: 0.8130 (tp30) REVERT: B 219 TYR cc_start: 0.7293 (t80) cc_final: 0.6801 (t80) REVERT: B 236 LEU cc_start: 0.9090 (tp) cc_final: 0.8859 (tp) REVERT: C 95 ASN cc_start: 0.9194 (t0) cc_final: 0.8913 (t0) REVERT: C 98 LEU cc_start: 0.8520 (mm) cc_final: 0.8123 (mm) REVERT: C 178 GLN cc_start: 0.9010 (pt0) cc_final: 0.8517 (pp30) REVERT: C 334 MET cc_start: 0.4810 (tpt) cc_final: 0.4521 (tpp) REVERT: D 71 TRP cc_start: 0.8049 (t60) cc_final: 0.7721 (t60) REVERT: D 88 LYS cc_start: 0.9574 (mmmt) cc_final: 0.8987 (mmmt) REVERT: D 91 LEU cc_start: 0.9244 (mt) cc_final: 0.8915 (mt) REVERT: D 147 MET cc_start: 0.9069 (ppp) cc_final: 0.8760 (ppp) REVERT: D 249 GLU cc_start: 0.8681 (pt0) cc_final: 0.8380 (pt0) REVERT: D 254 ASP cc_start: 0.8357 (m-30) cc_final: 0.8147 (m-30) outliers start: 2 outliers final: 1 residues processed: 173 average time/residue: 0.0815 time to fit residues: 21.0386 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS D 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.077939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.066843 restraints weight = 56730.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068515 restraints weight = 37580.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.069700 restraints weight = 27349.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070582 restraints weight = 21246.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071215 restraints weight = 17426.174| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10649 Z= 0.117 Angle : 0.595 7.828 14402 Z= 0.304 Chirality : 0.043 0.148 1615 Planarity : 0.004 0.050 1768 Dihedral : 4.598 17.524 1364 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.18 % Allowed : 0.44 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1256 helix: 0.89 (0.21), residues: 596 sheet: 1.14 (0.42), residues: 164 loop : -1.44 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 166 TYR 0.015 0.001 TYR D 138 PHE 0.023 0.001 PHE A 152 TRP 0.018 0.001 TRP D 26 HIS 0.009 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00253 (10649) covalent geometry : angle 0.59541 (14402) hydrogen bonds : bond 0.03858 ( 526) hydrogen bonds : angle 4.95698 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8615 (tp-100) cc_final: 0.8233 (tp40) REVERT: B 76 ASN cc_start: 0.8593 (t0) cc_final: 0.8168 (t0) REVERT: B 89 LYS cc_start: 0.9226 (ptpp) cc_final: 0.8839 (ptpp) REVERT: B 110 GLU cc_start: 0.8432 (tp30) cc_final: 0.8118 (tp30) REVERT: B 219 TYR cc_start: 0.7238 (t80) cc_final: 0.6693 (t80) REVERT: B 236 LEU cc_start: 0.9084 (tp) cc_final: 0.8855 (tp) REVERT: B 249 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7816 (pm20) REVERT: C 95 ASN cc_start: 0.9185 (t0) cc_final: 0.8896 (t0) REVERT: C 98 LEU cc_start: 0.8469 (mm) cc_final: 0.8046 (mm) REVERT: C 178 GLN cc_start: 0.9004 (pt0) cc_final: 0.8499 (pp30) REVERT: C 334 MET cc_start: 0.4795 (tpt) cc_final: 0.4498 (tpp) REVERT: D 80 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.7515 (ttp-170) REVERT: D 147 MET cc_start: 0.8998 (ppp) cc_final: 0.8561 (ppp) REVERT: D 249 GLU cc_start: 0.8560 (pt0) cc_final: 0.8337 (pt0) outliers start: 2 outliers final: 2 residues processed: 172 average time/residue: 0.0781 time to fit residues: 20.2313 Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 56 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 118 optimal weight: 0.0030 chunk 84 optimal weight: 0.0370 chunk 88 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 55 ASN C 107 ASN C 175 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.079373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.068172 restraints weight = 55463.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.069883 restraints weight = 36236.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071110 restraints weight = 26250.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.072004 restraints weight = 20393.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.072663 restraints weight = 16643.439| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10649 Z= 0.112 Angle : 0.600 7.857 14402 Z= 0.304 Chirality : 0.043 0.203 1615 Planarity : 0.004 0.043 1768 Dihedral : 4.449 16.433 1364 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.74 % 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: 0.11 (0.24), residues: 1256 helix: 0.97 (0.22), residues: 596 sheet: 1.19 (0.42), residues: 162 loop : -1.44 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 166 TYR 0.021 0.001 TYR D 63 PHE 0.025 0.001 PHE A 152 TRP 0.019 0.001 TRP D 26 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00237 (10649) covalent geometry : angle 0.60011 (14402) hydrogen bonds : bond 0.03695 ( 526) hydrogen bonds : angle 4.83991 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8591 (tp-100) cc_final: 0.8197 (tp40) REVERT: B 76 ASN cc_start: 0.8469 (t0) cc_final: 0.8088 (t0) REVERT: B 93 THR cc_start: 0.9106 (p) cc_final: 0.8902 (p) REVERT: B 110 GLU cc_start: 0.8414 (tp30) cc_final: 0.8051 (tp30) REVERT: B 114 TYR cc_start: 0.7951 (t80) cc_final: 0.7499 (t80) REVERT: B 219 TYR cc_start: 0.7344 (t80) cc_final: 0.6767 (t80) REVERT: C 95 ASN cc_start: 0.9198 (t0) cc_final: 0.8920 (t0) REVERT: C 98 LEU cc_start: 0.8304 (mm) cc_final: 0.7868 (mm) REVERT: C 334 MET cc_start: 0.4447 (tpt) cc_final: 0.4204 (tpp) REVERT: D 72 PHE cc_start: 0.8089 (m-10) cc_final: 0.7883 (m-80) REVERT: D 80 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.7570 (ttp-170) REVERT: D 147 MET cc_start: 0.9022 (ppp) cc_final: 0.8647 (ppp) REVERT: D 205 MET cc_start: 0.8938 (mmm) cc_final: 0.8617 (mmm) REVERT: D 249 GLU cc_start: 0.8502 (pt0) cc_final: 0.8301 (pt0) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.0794 time to fit residues: 23.0718 Evaluate side-chains 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 55 ASN C 175 HIS C 178 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.069075 restraints weight = 55950.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070806 restraints weight = 36716.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.072013 restraints weight = 26660.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072794 restraints weight = 20734.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.073532 restraints weight = 17326.403| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10649 Z= 0.110 Angle : 0.588 7.803 14402 Z= 0.298 Chirality : 0.043 0.234 1615 Planarity : 0.004 0.043 1768 Dihedral : 4.388 16.341 1364 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.24), residues: 1256 helix: 0.97 (0.22), residues: 595 sheet: 1.20 (0.42), residues: 162 loop : -1.38 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.018 0.001 TYR D 63 PHE 0.024 0.001 PHE A 152 TRP 0.017 0.001 TRP D 26 HIS 0.008 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00237 (10649) covalent geometry : angle 0.58823 (14402) hydrogen bonds : bond 0.03686 ( 526) hydrogen bonds : angle 4.81272 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.44 seconds wall clock time: 26 minutes 12.17 seconds (1572.17 seconds total)