Starting phenix.real_space_refine on Mon Jun 16 12:26:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl0_27494/06_2025/8dl0_27494.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl0_27494/06_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_27494/06_2025/8dl0_27494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl0_27494/06_2025/8dl0_27494.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl0_27494/06_2025/8dl0_27494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl0_27494/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.14, per 1000 atoms: 0.59 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: 2.20 Conformation dependent library (CDL) restraints added in 1.3 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: 1.00 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: 2.64 Time building geometry restraints manager: 2.67 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.990 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.920 ------------------------------------------------------------------------------- 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 : 1.285 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: 0.2098 time to fit residues: 57.8868 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 : 1.187 ------------------------------------------------------------------------------- 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 = 0.065915 restraints weight = 56651.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.067550 restraints weight = 37036.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068723 restraints weight = 26821.988| |-----------------------------------------------------------------------------| 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 : 3.602 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: 0.9166 (ptpp) cc_final: 0.8900 (pttm) REVERT: A 157 HIS cc_start: 0.8346 (m90) cc_final: 0.7850 (m90) REVERT: A 178 GLN cc_start: 0.8633 (tp-100) cc_final: 0.8201 (tp40) REVERT: B 76 ASN cc_start: 0.8579 (t0) cc_final: 0.8109 (t0) REVERT: B 110 GLU cc_start: 0.8386 (tp30) cc_final: 0.8165 (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: 0.6778 (t80) REVERT: C 95 ASN cc_start: 0.9112 (t0) cc_final: 0.8753 (t0) REVERT: C 98 LEU cc_start: 0.8621 (mm) cc_final: 0.8078 (mm) REVERT: D 80 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8215 (ttp-170) REVERT: D 205 MET cc_start: 0.8891 (mmm) cc_final: 0.8565 (mmm) REVERT: D 249 GLU cc_start: 0.8638 (pt0) cc_final: 0.8369 (pt0) outliers start: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2181 time to fit residues: 59.6562 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 : 1.095 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 0.0370 chunk 107 optimal weight: 0.7980 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: 7.9990 chunk 26 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.076394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065492 restraints weight = 58853.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.067072 restraints weight = 39187.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.068170 restraints weight = 28764.463| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10649 Z= 0.151 Angle : 0.574 6.084 14402 Z= 0.303 Chirality : 0.043 0.134 1615 Planarity : 0.004 0.061 1768 Dihedral : 4.716 18.190 1364 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: 0.17 (0.24), residues: 1256 helix: 1.00 (0.21), residues: 589 sheet: 1.29 (0.38), residues: 179 loop : -1.47 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 26 HIS 0.011 0.002 HIS B 213 PHE 0.026 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 0.04225 ( 526) hydrogen bonds : angle 5.35793 ( 1509) covalent geometry : bond 0.00326 (10649) covalent geometry : angle 0.57404 (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 178 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8939 (pttm) REVERT: A 157 HIS cc_start: 0.8312 (m90) cc_final: 0.7891 (m90) REVERT: A 178 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8230 (tp40) REVERT: B 76 ASN cc_start: 0.8573 (t0) cc_final: 0.8057 (t0) REVERT: B 110 GLU cc_start: 0.8377 (tp30) cc_final: 0.8082 (tp30) REVERT: B 114 TYR cc_start: 0.8255 (t80) cc_final: 0.7529 (t80) REVERT: B 169 LYS cc_start: 0.9097 (ptmm) cc_final: 0.8766 (tptp) REVERT: B 206 TYR cc_start: 0.8186 (t80) cc_final: 0.7930 (t80) REVERT: B 219 TYR cc_start: 0.7368 (t80) cc_final: 0.6769 (t80) REVERT: C 95 ASN cc_start: 0.9078 (t0) cc_final: 0.8694 (t0) REVERT: C 98 LEU cc_start: 0.8600 (mm) cc_final: 0.8024 (mm) REVERT: D 74 PHE cc_start: 0.8771 (t80) cc_final: 0.8567 (t80) REVERT: D 80 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8020 (ttp-170) REVERT: D 249 GLU cc_start: 0.8665 (pt0) cc_final: 0.8391 (pt0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2190 time to fit residues: 57.7007 Evaluate side-chains 126 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.077258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.066176 restraints weight = 57641.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.067769 restraints weight = 38396.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.068886 restraints weight = 28297.848| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2114 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= 0.126 Angle : 0.554 6.624 14402 Z= 0.290 Chirality : 0.042 0.139 1615 Planarity : 0.004 0.053 1768 Dihedral : 4.607 18.047 1364 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 1.10 (0.22), residues: 594 sheet: 1.24 (0.40), residues: 174 loop : -1.44 (0.27), residues: 488 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 0.015 0.001 TYR D 138 ARG 0.008 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 526) hydrogen bonds : angle 5.14905 ( 1509) covalent geometry : bond 0.00269 (10649) covalent geometry : angle 0.55419 (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 : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8834 (pttm) REVERT: A 157 HIS cc_start: 0.8282 (m90) cc_final: 0.8077 (m90) REVERT: A 178 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8239 (tp40) REVERT: B 76 ASN cc_start: 0.8625 (t0) cc_final: 0.8143 (t0) REVERT: B 110 GLU cc_start: 0.8441 (tp30) cc_final: 0.8094 (tp30) REVERT: B 169 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8810 (tptp) REVERT: B 219 TYR cc_start: 0.7355 (t80) cc_final: 0.6730 (t80) REVERT: C 95 ASN cc_start: 0.9143 (t0) cc_final: 0.8762 (t0) REVERT: C 98 LEU cc_start: 0.8533 (mm) cc_final: 0.8052 (mm) REVERT: C 178 GLN cc_start: 0.8953 (pt0) cc_final: 0.8562 (pp30) REVERT: D 71 TRP cc_start: 0.8224 (t60) cc_final: 0.8011 (t60) REVERT: D 80 ARG cc_start: 0.8853 (tmm-80) cc_final: 0.7966 (ttp-170) REVERT: D 249 GLU cc_start: 0.8569 (pt0) cc_final: 0.8333 (pt0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1899 time to fit residues: 50.3134 Evaluate side-chains 123 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 4.9990 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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** C 175 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.076228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065337 restraints weight = 57442.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.066920 restraints weight = 38307.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.068047 restraints weight = 28144.634| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10649 Z= 0.157 Angle : 0.591 7.072 14402 Z= 0.311 Chirality : 0.043 0.167 1615 Planarity : 0.004 0.049 1768 Dihedral : 4.755 18.519 1364 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.94 (0.21), residues: 597 sheet: 1.19 (0.41), residues: 174 loop : -1.47 (0.27), residues: 485 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 0.023 0.002 PHE D 72 TYR 0.018 0.001 TYR D 138 ARG 0.008 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 526) hydrogen bonds : angle 5.19205 ( 1509) covalent geometry : bond 0.00343 (10649) covalent geometry : angle 0.59064 (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 175 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8262 (tp40) REVERT: B 76 ASN cc_start: 0.8614 (t0) cc_final: 0.8056 (t0) REVERT: B 114 TYR cc_start: 0.8073 (t80) cc_final: 0.7556 (t80) REVERT: B 169 LYS cc_start: 0.9076 (ptmm) cc_final: 0.8760 (tptp) REVERT: B 219 TYR cc_start: 0.7419 (t80) cc_final: 0.6787 (t80) REVERT: C 95 ASN cc_start: 0.9146 (t0) cc_final: 0.8765 (t0) REVERT: C 98 LEU cc_start: 0.8517 (mm) cc_final: 0.8009 (mm) REVERT: C 178 GLN cc_start: 0.8937 (pt0) cc_final: 0.8578 (pp30) REVERT: D 80 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.7663 (ttp-170) REVERT: D 205 MET cc_start: 0.8971 (mmm) cc_final: 0.8756 (mmm) REVERT: D 249 GLU cc_start: 0.8728 (pt0) cc_final: 0.8476 (pt0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1891 time to fit residues: 48.8437 Evaluate side-chains 123 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 93 optimal weight: 0.1980 chunk 24 optimal weight: 8.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 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 = 0.3622 r_free = 0.3622 target = 0.077331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066259 restraints weight = 57090.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.067928 restraints weight = 37343.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.069098 restraints weight = 27090.996| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 10649 Z= 0.121 Angle : 0.564 7.842 14402 Z= 0.294 Chirality : 0.042 0.138 1615 Planarity : 0.004 0.050 1768 Dihedral : 4.603 17.809 1364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.09 % Allowed : 1.93 % Favored : 97.98 % 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: 1.12 (0.22), residues: 595 sheet: 1.23 (0.41), residues: 167 loop : -1.43 (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 0.022 0.001 PHE A 152 TYR 0.015 0.001 TYR D 138 ARG 0.008 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 526) hydrogen bonds : angle 5.04607 ( 1509) covalent geometry : bond 0.00266 (10649) covalent geometry : angle 0.56410 (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 173 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8358 (m90) cc_final: 0.7692 (m90) REVERT: A 178 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8238 (tp40) REVERT: B 76 ASN cc_start: 0.8613 (t0) cc_final: 0.8137 (t0) REVERT: B 114 TYR cc_start: 0.8097 (t80) cc_final: 0.7436 (t80) REVERT: B 169 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8812 (tptp) REVERT: C 95 ASN cc_start: 0.9156 (t0) cc_final: 0.8778 (t0) REVERT: C 98 LEU cc_start: 0.8486 (mm) cc_final: 0.7913 (mm) REVERT: C 178 GLN cc_start: 0.8996 (pt0) cc_final: 0.8540 (pp30) REVERT: C 334 MET cc_start: 0.4647 (tpt) cc_final: 0.4446 (tpp) REVERT: D 80 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.7499 (ttp-170) REVERT: D 249 GLU cc_start: 0.8682 (pt0) cc_final: 0.8346 (pt0) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.2017 time to fit residues: 51.1842 Evaluate side-chains 124 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.074665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.063645 restraints weight = 58922.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065246 restraints weight = 38967.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066379 restraints weight = 28358.690| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10649 Z= 0.204 Angle : 0.654 7.452 14402 Z= 0.343 Chirality : 0.044 0.142 1615 Planarity : 0.004 0.067 1768 Dihedral : 4.985 18.908 1364 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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 (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: -0.07 (0.24), residues: 1256 helix: 0.77 (0.21), residues: 599 sheet: 0.90 (0.40), residues: 174 loop : -1.44 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 26 HIS 0.007 0.002 HIS C 175 PHE 0.023 0.002 PHE B 137 TYR 0.020 0.002 TYR D 138 ARG 0.011 0.001 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 526) hydrogen bonds : angle 5.38029 ( 1509) covalent geometry : bond 0.00446 (10649) covalent geometry : angle 0.65427 (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 160 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 HIS cc_start: 0.8422 (m90) cc_final: 0.7937 (m90) REVERT: A 178 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8328 (tp40) REVERT: B 76 ASN cc_start: 0.8583 (t0) cc_final: 0.8339 (t0) REVERT: B 114 TYR cc_start: 0.8268 (t80) cc_final: 0.7396 (t80) REVERT: B 169 LYS cc_start: 0.9117 (ptmm) cc_final: 0.8814 (tptp) REVERT: B 236 LEU cc_start: 0.9104 (tp) cc_final: 0.8858 (tp) REVERT: B 251 ASP cc_start: 0.8481 (t70) cc_final: 0.8249 (t0) REVERT: C 178 GLN cc_start: 0.9007 (pt0) cc_final: 0.8572 (pp30) REVERT: D 88 LYS cc_start: 0.9624 (mmmt) cc_final: 0.9003 (mmmt) REVERT: D 91 LEU cc_start: 0.9270 (mt) cc_final: 0.8978 (mt) REVERT: D 249 GLU cc_start: 0.8616 (pt0) cc_final: 0.8254 (pt0) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1986 time to fit residues: 46.7055 Evaluate side-chains 112 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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: 5.9990 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3612 r_free = 0.3612 target = 0.076475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065312 restraints weight = 56830.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066995 restraints weight = 37295.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068202 restraints weight = 26913.990| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10649 Z= 0.121 Angle : 0.588 7.433 14402 Z= 0.305 Chirality : 0.043 0.166 1615 Planarity : 0.004 0.056 1768 Dihedral : 4.657 18.093 1364 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 0.02 (0.24), residues: 1256 helix: 0.90 (0.21), residues: 603 sheet: 1.08 (0.42), residues: 162 loop : -1.49 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.006 0.001 HIS B 213 PHE 0.024 0.001 PHE A 152 TYR 0.016 0.001 TYR D 138 ARG 0.009 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 526) hydrogen bonds : angle 5.10669 ( 1509) covalent geometry : bond 0.00267 (10649) covalent geometry : angle 0.58815 (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 176 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8275 (tp40) REVERT: B 76 ASN cc_start: 0.8590 (t0) cc_final: 0.8187 (t0) REVERT: B 169 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8856 (tptp) REVERT: B 212 HIS cc_start: 0.8000 (m90) cc_final: 0.7791 (m90) REVERT: B 236 LEU cc_start: 0.9100 (tp) cc_final: 0.8878 (tp) REVERT: B 251 ASP cc_start: 0.8463 (t70) cc_final: 0.8218 (t0) REVERT: C 95 ASN cc_start: 0.9152 (t0) cc_final: 0.8859 (t0) REVERT: C 98 LEU cc_start: 0.8509 (mm) cc_final: 0.8054 (mm) REVERT: C 178 GLN cc_start: 0.9051 (pt0) cc_final: 0.8534 (pp30) REVERT: C 334 MET cc_start: 0.4965 (tpt) cc_final: 0.4652 (tpp) REVERT: D 80 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.7432 (ttp-170) REVERT: D 88 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9131 (mmmt) REVERT: D 147 MET cc_start: 0.9095 (ppp) cc_final: 0.8749 (ppp) REVERT: D 249 GLU cc_start: 0.8621 (pt0) cc_final: 0.8274 (pt0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1965 time to fit residues: 51.4835 Evaluate side-chains 116 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS C 175 HIS ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 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 = 0.3592 r_free = 0.3592 target = 0.075601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.064618 restraints weight = 58319.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066231 restraints weight = 38189.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067401 restraints weight = 27697.528| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 0.077 10649 Z= 0.157 Angle : 0.622 9.054 14402 Z= 0.322 Chirality : 0.044 0.202 1615 Planarity : 0.004 0.059 1768 Dihedral : 4.778 18.502 1364 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.18 % Allowed : 0.79 % Favored : 99.03 % 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: -0.04 (0.24), residues: 1256 helix: 0.83 (0.21), residues: 598 sheet: 0.95 (0.41), residues: 166 loop : -1.46 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.010 0.001 HIS C 175 PHE 0.023 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 0.04187 ( 526) hydrogen bonds : angle 5.21788 ( 1509) covalent geometry : bond 0.00347 (10649) covalent geometry : angle 0.62197 (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 164 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8280 (tp40) REVERT: B 76 ASN cc_start: 0.8551 (t0) cc_final: 0.8243 (t0) REVERT: B 169 LYS cc_start: 0.9150 (ptmm) cc_final: 0.8880 (tptp) REVERT: B 212 HIS cc_start: 0.8012 (m90) cc_final: 0.7731 (m90) REVERT: B 236 LEU cc_start: 0.9092 (tp) cc_final: 0.8860 (tp) REVERT: B 251 ASP cc_start: 0.8495 (t70) cc_final: 0.8221 (t0) REVERT: C 95 ASN cc_start: 0.9190 (t0) cc_final: 0.8910 (t0) REVERT: C 98 LEU cc_start: 0.8551 (mm) cc_final: 0.8123 (mm) REVERT: C 178 GLN cc_start: 0.9022 (pt0) cc_final: 0.8547 (pp30) REVERT: C 334 MET cc_start: 0.5385 (tpt) cc_final: 0.5036 (tpp) REVERT: D 80 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.7730 (ttp-170) REVERT: D 88 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9095 (mmmt) REVERT: D 91 LEU cc_start: 0.9280 (mt) cc_final: 0.8914 (mt) REVERT: D 249 GLU cc_start: 0.8589 (pt0) cc_final: 0.8262 (pt0) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.1860 time to fit residues: 46.0110 Evaluate side-chains 123 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 110 optimal weight: 0.0170 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 overall best weight: 1.1022 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.077363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066237 restraints weight = 57629.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.067901 restraints weight = 37865.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.069076 restraints weight = 27516.836| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10649 Z= 0.118 Angle : 0.588 7.841 14402 Z= 0.303 Chirality : 0.043 0.190 1615 Planarity : 0.004 0.050 1768 Dihedral : 4.578 17.625 1364 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.21), residues: 603 sheet: 1.06 (0.42), residues: 166 loop : -1.53 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 26 HIS 0.005 0.001 HIS C 355 PHE 0.023 0.001 PHE A 152 TYR 0.015 0.001 TYR D 63 ARG 0.008 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 526) hydrogen bonds : angle 5.03428 ( 1509) covalent geometry : bond 0.00261 (10649) covalent geometry : angle 0.58803 (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 172 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8262 (tp40) REVERT: B 76 ASN cc_start: 0.8522 (t0) cc_final: 0.8207 (t0) REVERT: B 169 LYS cc_start: 0.9162 (ptmm) cc_final: 0.8894 (tptp) REVERT: B 236 LEU cc_start: 0.9061 (tp) cc_final: 0.8837 (tp) REVERT: B 251 ASP cc_start: 0.8433 (t70) cc_final: 0.8128 (t0) REVERT: C 95 ASN cc_start: 0.9182 (t0) cc_final: 0.8912 (t0) REVERT: C 98 LEU cc_start: 0.8413 (mm) cc_final: 0.7991 (mm) REVERT: C 178 GLN cc_start: 0.9069 (pt0) cc_final: 0.8516 (pp30) REVERT: C 334 MET cc_start: 0.5245 (tpt) cc_final: 0.4996 (tpp) REVERT: D 71 TRP cc_start: 0.8079 (t60) cc_final: 0.7750 (t60) REVERT: D 80 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.7581 (ttp-170) REVERT: D 88 LYS cc_start: 0.9544 (mmmt) cc_final: 0.9080 (mmmt) REVERT: D 91 LEU cc_start: 0.9255 (mt) cc_final: 0.8867 (mt) REVERT: D 147 MET cc_start: 0.9115 (ppp) cc_final: 0.8804 (ppp) REVERT: D 249 GLU cc_start: 0.8537 (pt0) cc_final: 0.8209 (pt0) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1804 time to fit residues: 46.6452 Evaluate side-chains 128 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 HIS ** 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 = 0.3617 r_free = 0.3617 target = 0.077017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066172 restraints weight = 57639.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.067762 restraints weight = 38274.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068902 restraints weight = 27954.386| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10649 Z= 0.126 Angle : 0.602 9.771 14402 Z= 0.311 Chirality : 0.044 0.216 1615 Planarity : 0.004 0.048 1768 Dihedral : 4.621 24.403 1364 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % 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: 0.01 (0.24), residues: 1256 helix: 0.93 (0.21), residues: 601 sheet: 1.08 (0.42), residues: 165 loop : -1.57 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 26 HIS 0.010 0.001 HIS A 187 PHE 0.022 0.002 PHE A 152 TYR 0.017 0.001 TYR D 63 ARG 0.007 0.000 ARG B 166 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 526) hydrogen bonds : angle 5.05015 ( 1509) covalent geometry : bond 0.00278 (10649) covalent geometry : angle 0.60171 (14402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.06 seconds wall clock time: 53 minutes 50.21 seconds (3230.21 seconds total)