Starting phenix.real_space_refine on Mon May 19 14:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl0_27494/05_2025/8dl0_27494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl0_27494/05_2025/8dl0_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_27494/05_2025/8dl0_27494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl0_27494/05_2025/8dl0_27494.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl0_27494/05_2025/8dl0_27494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl0_27494/05_2025/8dl0_27494.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.56, per 1000 atoms: 0.63 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.06 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: 2.66 Time building geometry restraints manager: 2.80 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.610 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP D 26 HIS 0.007 0.001 HIS A 361 PHE 0.032 0.001 PHE B 244 TYR 0.014 0.001 TYR D 18 ARG 0.005 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.16373 ( 526) hydrogen bonds : angle 6.98919 ( 1509) covalent geometry : bond 0.00269 (10649) covalent geometry : angle 0.66752 (14402) *********************** 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 : 1.090 Fit side-chains revert: symmetry clash 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: 0.7972 (m-70) REVERT: B 76 ASN cc_start: 0.8180 (t0) cc_final: 0.7807 (t0) REVERT: B 89 LYS cc_start: 0.9479 (ptmt) cc_final: 0.9090 (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: 0.8165 (tp30) REVERT: B 113 ASN cc_start: 0.8539 (p0) cc_final: 0.8279 (p0) REVERT: B 169 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8671 (tptp) REVERT: B 206 TYR cc_start: 0.8138 (t80) cc_final: 0.7863 (t80) REVERT: B 219 TYR cc_start: 0.7320 (t80) cc_final: 0.6719 (t80) REVERT: B 236 LEU cc_start: 0.9107 (tp) cc_final: 0.8870 (tp) REVERT: C 98 LEU cc_start: 0.8571 (mm) cc_final: 0.8320 (mm) REVERT: C 334 MET cc_start: 0.6261 (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: 0.8705 (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: 0.1871 time to fit residues: 51.3339 Evaluate side-chains 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS C 175 HIS ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3618 r_free = 0.3618 target = 0.076887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065914 restraints weight = 56651.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067549 restraints weight = 37038.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068719 restraints weight = 26823.484| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1393 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= 0.163 Angle : 0.594 6.881 14402 Z= 0.316 Chirality : 0.043 0.141 1615 Planarity : 0.004 0.044 1768 Dihedral : 4.665 18.698 1364 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.18 % Allowed : 4.39 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1256 helix: 1.09 (0.22), residues: 592 sheet: 1.20 (0.38), residues: 181 loop : -1.48 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 26 HIS 0.009 0.002 HIS D 213 PHE 0.025 0.002 PHE D 72 TYR 0.016 0.001 TYR D 138 ARG 0.007 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 526) hydrogen bonds : angle 5.57009 ( 1509) covalent geometry : bond 0.00349 (10649) covalent geometry : angle 0.59390 (14402) *********************** 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 184 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 182 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8901 (pttm) REVERT: A 157 HIS cc_start: 0.8343 (m90) cc_final: 0.7847 (m90) REVERT: A 178 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8201 (tp40) REVERT: B 76 ASN cc_start: 0.8579 (t0) cc_final: 0.8108 (t0) REVERT: B 110 GLU cc_start: 0.8385 (tp30) cc_final: 0.8163 (tp30) REVERT: B 169 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8786 (tptp) REVERT: B 219 TYR cc_start: 0.7334 (t80) cc_final: 0.6779 (t80) REVERT: C 95 ASN cc_start: 0.9113 (t0) cc_final: 0.8752 (t0) REVERT: C 98 LEU cc_start: 0.8621 (mm) cc_final: 0.8078 (mm) REVERT: D 80 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8215 (ttp-170) REVERT: D 205 MET cc_start: 0.8891 (mmm) cc_final: 0.8564 (mmm) REVERT: D 249 GLU cc_start: 0.8639 (pt0) cc_final: 0.8368 (pt0) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2150 time to fit residues: 56.7303 Evaluate side-chains 132 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 0.0870 chunk 26 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN C 178 GLN ** C 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3613 r_free = 0.3613 target = 0.076539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.065650 restraints weight = 58575.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067225 restraints weight = 39064.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068325 restraints weight = 28722.936| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1846 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= 0.151 Angle : 0.573 6.004 14402 Z= 0.302 Chirality : 0.043 0.136 1615 Planarity : 0.004 0.060 1768 Dihedral : 4.701 18.287 1364 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1256 helix: 1.01 (0.21), residues: 589 sheet: 1.30 (0.38), residues: 179 loop : -1.47 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 26 HIS 0.011 0.001 HIS B 213 PHE 0.025 0.002 PHE A 152 TYR 0.016 0.001 TYR D 138 ARG 0.008 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 526) hydrogen bonds : angle 5.36426 ( 1509) covalent geometry : bond 0.00327 (10649) covalent geometry : angle 0.57345 (14402) *********************** 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 177 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8936 (pttm) REVERT: A 157 HIS cc_start: 0.8336 (m90) cc_final: 0.7808 (m90) REVERT: A 178 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8217 (tp40) REVERT: B 76 ASN cc_start: 0.8575 (t0) cc_final: 0.8040 (t0) REVERT: B 110 GLU cc_start: 0.8387 (tp30) cc_final: 0.8092 (tp30) REVERT: B 114 TYR cc_start: 0.8223 (t80) cc_final: 0.7518 (t80) REVERT: B 169 LYS cc_start: 0.9098 (ptmm) cc_final: 0.8765 (tptp) REVERT: B 206 TYR cc_start: 0.8213 (t80) cc_final: 0.7962 (t80) REVERT: B 219 TYR cc_start: 0.7359 (t80) cc_final: 0.6758 (t80) REVERT: C 95 ASN cc_start: 0.9080 (t0) cc_final: 0.8695 (t0) REVERT: C 98 LEU cc_start: 0.8599 (mm) cc_final: 0.8026 (mm) REVERT: D 74 PHE cc_start: 0.8779 (t80) cc_final: 0.8568 (t80) REVERT: D 80 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.8007 (ttp-170) REVERT: D 249 GLU cc_start: 0.8666 (pt0) cc_final: 0.8393 (pt0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2110 time to fit residues: 55.2638 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065606 restraints weight = 56380.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067244 restraints weight = 37016.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068426 restraints weight = 26854.077| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10649 Z= 0.129 Angle : 0.557 7.370 14402 Z= 0.292 Chirality : 0.042 0.139 1615 Planarity : 0.004 0.052 1768 Dihedral : 4.625 18.034 1364 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1256 helix: 1.12 (0.22), residues: 588 sheet: 1.30 (0.39), residues: 181 loop : -1.39 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 26 HIS 0.007 0.001 HIS B 213 PHE 0.024 0.002 PHE A 152 TYR 0.016 0.001 TYR A 105 ARG 0.008 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 526) hydrogen bonds : angle 5.18723 ( 1509) covalent geometry : bond 0.00279 (10649) covalent geometry : angle 0.55721 (14402) *********************** 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 180 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9188 (ptpp) cc_final: 0.8855 (pttm) REVERT: A 157 HIS cc_start: 0.8316 (m90) cc_final: 0.8060 (m90) REVERT: A 178 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8239 (tp40) REVERT: B 76 ASN cc_start: 0.8618 (t0) cc_final: 0.8161 (t0) REVERT: B 110 GLU cc_start: 0.8476 (tp30) cc_final: 0.8150 (tp30) REVERT: B 169 LYS cc_start: 0.9118 (ptmm) cc_final: 0.8792 (tptp) REVERT: B 219 TYR cc_start: 0.7373 (t80) cc_final: 0.6765 (t80) REVERT: C 95 ASN cc_start: 0.9137 (t0) cc_final: 0.8767 (t0) REVERT: C 98 LEU cc_start: 0.8532 (mm) cc_final: 0.8052 (mm) REVERT: C 178 GLN cc_start: 0.8974 (pt0) cc_final: 0.8575 (pp30) REVERT: D 72 PHE cc_start: 0.8163 (m-80) cc_final: 0.7962 (m-80) REVERT: D 80 ARG cc_start: 0.8823 (tmm-80) cc_final: 0.7959 (ttp-170) REVERT: D 249 GLU cc_start: 0.8646 (pt0) cc_final: 0.8383 (pt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1948 time to fit residues: 51.3763 Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.075525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.064607 restraints weight = 58210.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066227 restraints weight = 38684.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067372 restraints weight = 28198.592| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10649 Z= 0.172 Angle : 0.607 6.627 14402 Z= 0.321 Chirality : 0.044 0.172 1615 Planarity : 0.004 0.060 1768 Dihedral : 4.844 18.727 1364 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1256 helix: 0.90 (0.21), residues: 597 sheet: 1.15 (0.41), residues: 174 loop : -1.48 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 26 HIS 0.007 0.002 HIS B 213 PHE 0.023 0.002 PHE A 152 TYR 0.019 0.001 TYR D 138 ARG 0.009 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 526) hydrogen bonds : angle 5.26517 ( 1509) covalent geometry : bond 0.00374 (10649) covalent geometry : angle 0.60741 (14402) *********************** 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 167 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8302 (m90) cc_final: 0.8081 (m90) REVERT: A 178 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8292 (tp40) REVERT: B 76 ASN cc_start: 0.8566 (t0) cc_final: 0.8129 (t0) REVERT: B 110 GLU cc_start: 0.8489 (tp30) cc_final: 0.8041 (tp30) REVERT: B 114 TYR cc_start: 0.8129 (t80) cc_final: 0.7604 (t80) REVERT: B 169 LYS cc_start: 0.9103 (ptmm) cc_final: 0.8791 (tptp) REVERT: B 219 TYR cc_start: 0.7407 (t80) cc_final: 0.6797 (t80) REVERT: C 95 ASN cc_start: 0.9160 (t0) cc_final: 0.8771 (t0) REVERT: C 98 LEU cc_start: 0.8471 (mm) cc_final: 0.7905 (mm) REVERT: C 178 GLN cc_start: 0.8945 (pt0) cc_final: 0.8597 (pp30) REVERT: D 80 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.7650 (ttp-170) REVERT: D 249 GLU cc_start: 0.8795 (pt0) cc_final: 0.8510 (pt0) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1940 time to fit residues: 47.6858 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 : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 53 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN C 175 HIS C 268 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 = 0.3635 r_free = 0.3635 target = 0.078206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.067105 restraints weight = 56280.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.068787 restraints weight = 37067.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069973 restraints weight = 27003.067| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 10649 Z= 0.110 Angle : 0.559 6.989 14402 Z= 0.292 Chirality : 0.042 0.140 1615 Planarity : 0.004 0.049 1768 Dihedral : 4.509 17.634 1364 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.09 % Allowed : 1.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1256 helix: 1.17 (0.22), residues: 595 sheet: 1.45 (0.42), residues: 159 loop : -1.48 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.007 0.001 HIS A 361 PHE 0.024 0.001 PHE A 152 TYR 0.013 0.001 TYR D 138 ARG 0.007 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 526) hydrogen bonds : angle 4.96543 ( 1509) covalent geometry : bond 0.00235 (10649) covalent geometry : angle 0.55885 (14402) *********************** 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 179 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8191 (tp40) REVERT: B 76 ASN cc_start: 0.8528 (t0) cc_final: 0.7960 (t0) REVERT: B 114 TYR cc_start: 0.8184 (t80) cc_final: 0.7573 (t80) REVERT: B 169 LYS cc_start: 0.9123 (ptmm) cc_final: 0.8836 (tptp) REVERT: C 95 ASN cc_start: 0.9207 (t0) cc_final: 0.8834 (t0) REVERT: C 98 LEU cc_start: 0.8450 (mm) cc_final: 0.7969 (mm) REVERT: C 178 GLN cc_start: 0.8966 (pt0) cc_final: 0.8551 (pp30) REVERT: C 334 MET cc_start: 0.4576 (tpt) cc_final: 0.4372 (tpp) REVERT: D 80 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.7417 (ttp-170) REVERT: D 88 LYS cc_start: 0.9537 (mmmt) cc_final: 0.9015 (mmmt) REVERT: D 91 LEU cc_start: 0.9233 (mt) cc_final: 0.8938 (mt) REVERT: D 249 GLU cc_start: 0.8587 (pt0) cc_final: 0.8261 (pt0) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1944 time to fit residues: 50.8417 Evaluate side-chains 127 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 103 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.076053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065018 restraints weight = 58944.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066653 restraints weight = 39049.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067816 restraints weight = 28512.493| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10649 Z= 0.166 Angle : 0.613 6.688 14402 Z= 0.320 Chirality : 0.044 0.133 1615 Planarity : 0.004 0.055 1768 Dihedral : 4.729 18.360 1364 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1256 helix: 0.93 (0.21), residues: 594 sheet: 1.08 (0.41), residues: 172 loop : -1.42 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 26 HIS 0.007 0.001 HIS B 213 PHE 0.022 0.002 PHE A 152 TYR 0.018 0.001 TYR D 138 ARG 0.009 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 526) hydrogen bonds : angle 5.17034 ( 1509) covalent geometry : bond 0.00368 (10649) covalent geometry : angle 0.61344 (14402) *********************** 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 163 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8268 (tp40) REVERT: B 76 ASN cc_start: 0.8585 (t0) cc_final: 0.8145 (t0) REVERT: B 114 TYR cc_start: 0.8230 (t80) cc_final: 0.7538 (t80) REVERT: B 169 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8842 (tptp) REVERT: B 212 HIS cc_start: 0.8034 (m90) cc_final: 0.7754 (m90) REVERT: B 236 LEU cc_start: 0.9099 (tp) cc_final: 0.8871 (tp) REVERT: C 178 GLN cc_start: 0.9029 (pt0) cc_final: 0.8523 (pp30) REVERT: C 334 MET cc_start: 0.4959 (tpt) cc_final: 0.4758 (tpp) REVERT: D 249 GLU cc_start: 0.8675 (pt0) cc_final: 0.8358 (pt0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1805 time to fit residues: 43.9584 Evaluate side-chains 114 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 32 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 112 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.077557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066547 restraints weight = 56344.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.068170 restraints weight = 37200.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.069393 restraints weight = 27201.446| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10649 Z= 0.115 Angle : 0.579 7.153 14402 Z= 0.298 Chirality : 0.043 0.170 1615 Planarity : 0.004 0.049 1768 Dihedral : 4.509 17.572 1364 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.09 % Allowed : 1.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1256 helix: 0.97 (0.21), residues: 602 sheet: 1.27 (0.42), residues: 162 loop : -1.50 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.007 0.001 HIS C 175 PHE 0.026 0.001 PHE A 152 TYR 0.014 0.001 TYR D 138 ARG 0.008 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 526) hydrogen bonds : angle 4.96214 ( 1509) covalent geometry : bond 0.00252 (10649) covalent geometry : angle 0.57899 (14402) *********************** 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 177 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8214 (tp40) REVERT: B 76 ASN cc_start: 0.8550 (t0) cc_final: 0.7995 (t0) REVERT: B 114 TYR cc_start: 0.8302 (t80) cc_final: 0.7459 (t80) REVERT: B 169 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8834 (tptp) REVERT: B 236 LEU cc_start: 0.9076 (tp) cc_final: 0.8844 (tp) REVERT: B 251 ASP cc_start: 0.8462 (t70) cc_final: 0.8173 (t0) REVERT: C 95 ASN cc_start: 0.9118 (t0) cc_final: 0.8753 (t0) REVERT: C 98 LEU cc_start: 0.8412 (mm) cc_final: 0.7874 (mm) REVERT: C 178 GLN cc_start: 0.8980 (pt0) cc_final: 0.8512 (pp30) REVERT: D 147 MET cc_start: 0.9059 (ppp) cc_final: 0.8735 (ppp) REVERT: D 249 GLU cc_start: 0.8622 (pt0) cc_final: 0.8375 (pt0) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1896 time to fit residues: 49.7835 Evaluate side-chains 125 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.077794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.066606 restraints weight = 57175.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068299 restraints weight = 37418.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069499 restraints weight = 27136.531| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10649 Z= 0.116 Angle : 0.585 7.475 14402 Z= 0.301 Chirality : 0.043 0.142 1615 Planarity : 0.004 0.046 1768 Dihedral : 4.476 17.209 1364 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1256 helix: 0.98 (0.21), residues: 600 sheet: 1.26 (0.42), residues: 162 loop : -1.47 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 26 HIS 0.006 0.001 HIS B 213 PHE 0.024 0.001 PHE A 152 TYR 0.014 0.001 TYR D 63 ARG 0.006 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 526) hydrogen bonds : angle 4.95661 ( 1509) covalent geometry : bond 0.00256 (10649) covalent geometry : angle 0.58548 (14402) *********************** 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: 0 poor density : 173 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8209 (tp40) REVERT: B 76 ASN cc_start: 0.8436 (t0) cc_final: 0.8005 (t0) REVERT: B 114 TYR cc_start: 0.8237 (t80) cc_final: 0.7495 (t80) REVERT: B 169 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8884 (tptp) REVERT: B 212 HIS cc_start: 0.8038 (m90) cc_final: 0.7816 (m90) REVERT: B 236 LEU cc_start: 0.9097 (tp) cc_final: 0.8878 (tp) REVERT: B 251 ASP cc_start: 0.8432 (t70) cc_final: 0.8145 (t0) REVERT: C 95 ASN cc_start: 0.9139 (t0) cc_final: 0.8848 (t0) REVERT: C 98 LEU cc_start: 0.8410 (mm) cc_final: 0.7960 (mm) REVERT: C 178 GLN cc_start: 0.9046 (pt0) cc_final: 0.8498 (pp30) REVERT: D 249 GLU cc_start: 0.8502 (pt0) cc_final: 0.8295 (pt0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1812 time to fit residues: 46.9414 Evaluate side-chains 127 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 40 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS C 175 HIS ** D 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.078318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067343 restraints weight = 57098.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068948 restraints weight = 38215.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.070100 restraints weight = 28043.064| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10649 Z= 0.117 Angle : 0.590 7.908 14402 Z= 0.304 Chirality : 0.043 0.204 1615 Planarity : 0.004 0.045 1768 Dihedral : 4.450 17.026 1364 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.09 % Allowed : 0.26 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1256 helix: 1.00 (0.21), residues: 600 sheet: 1.29 (0.42), residues: 162 loop : -1.54 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.008 0.001 HIS C 175 PHE 0.029 0.001 PHE D 72 TYR 0.017 0.001 TYR D 63 ARG 0.006 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 526) hydrogen bonds : angle 4.91779 ( 1509) covalent geometry : bond 0.00259 (10649) covalent geometry : angle 0.59045 (14402) ********************** 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 169 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8147 (tp40) REVERT: B 76 ASN cc_start: 0.8445 (t0) cc_final: 0.8014 (t0) REVERT: B 114 TYR cc_start: 0.8201 (t80) cc_final: 0.7601 (t80) REVERT: B 169 LYS cc_start: 0.9148 (ptmm) cc_final: 0.8900 (tptp) REVERT: B 212 HIS cc_start: 0.7946 (m90) cc_final: 0.7725 (m90) REVERT: B 236 LEU cc_start: 0.9101 (tp) cc_final: 0.8880 (tp) REVERT: C 95 ASN cc_start: 0.9180 (t0) cc_final: 0.8879 (t0) REVERT: C 98 LEU cc_start: 0.8359 (mm) cc_final: 0.7925 (mm) REVERT: C 178 GLN cc_start: 0.8963 (pt0) cc_final: 0.8469 (pp30) REVERT: D 147 MET cc_start: 0.9042 (ppp) cc_final: 0.8713 (ppp) REVERT: D 249 GLU cc_start: 0.8407 (pt0) cc_final: 0.8134 (pt0) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.1790 time to fit residues: 44.9541 Evaluate side-chains 129 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 124 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 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 = 0.3579 r_free = 0.3579 target = 0.075018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.064283 restraints weight = 59047.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065846 restraints weight = 39307.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.066944 restraints weight = 28778.149| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10649 Z= 0.210 Angle : 0.668 7.923 14402 Z= 0.350 Chirality : 0.045 0.171 1615 Planarity : 0.004 0.057 1768 Dihedral : 4.897 18.630 1364 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1256 helix: 0.77 (0.21), residues: 592 sheet: 0.95 (0.42), residues: 171 loop : -1.36 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 26 HIS 0.005 0.002 HIS C 31 PHE 0.024 0.002 PHE B 137 TYR 0.019 0.002 TYR D 63 ARG 0.009 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 526) hydrogen bonds : angle 5.27631 ( 1509) covalent geometry : bond 0.00460 (10649) covalent geometry : angle 0.66815 (14402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.62 seconds wall clock time: 51 minutes 42.10 seconds (3102.10 seconds total)