Starting phenix.real_space_refine on Tue Jun 10 18:34:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386.map" model { file = "/net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c20_16386/06_2025/8c20_16386_trim.cif" } resolution = 3.5 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= -0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7759 2.51 5 N 1885 2.21 5 O 2025 1.98 5 H 207 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11908 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 3020 Classifications: {'peptide': 358} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 337} Chain breaks: 3 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 3005 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 335} Chain breaks: 4 Chain: "C" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2857 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 323} Chain breaks: 8 Chain: "D" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 3000 Classifications: {'peptide': 355} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 335} Chain breaks: 4 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.70, per 1000 atoms: 0.65 Number of scatterers: 11908 At special positions: 0 Unit cell: (94.581, 94.581, 132.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2025 8.00 N 1885 7.00 C 7759 6.00 H 207 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 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: 3.02 Conformation dependent library (CDL) restraints added in 1.5 seconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2738 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 44.5% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.719A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 271 removed outlier: 3.810A pdb=" N VAL A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.859A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 318 through 333 removed outlier: 4.427A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TRP A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 459 Processing helix chain 'B' and resid 12 through 23 removed outlier: 4.082A pdb=" N ASN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.792A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 244 removed outlier: 4.224A pdb=" N PHE B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 273 removed outlier: 3.615A pdb=" N PHE B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 309 removed outlier: 3.869A pdb=" N PHE B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.654A pdb=" N LEU B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 462 Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.049A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.734A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 177' Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.905A pdb=" N SER C 226 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 Processing helix chain 'C' and resid 248 through 273 removed outlier: 3.681A pdb=" N VAL C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 285 through 310 removed outlier: 3.989A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 Processing helix chain 'C' and resid 421 through 462 removed outlier: 3.552A pdb=" N SER C 462 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 138 through 142 removed outlier: 4.151A pdb=" N ASN D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.583A pdb=" N VAL D 264 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 309 removed outlier: 3.593A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 329 removed outlier: 3.790A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 462 removed outlier: 3.620A pdb=" N LEU D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.993A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.993A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY A 121 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.572A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.936A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.896A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.672A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.672A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 89 removed outlier: 3.520A pdb=" N LEU C 86 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA C 134 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE C 103 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 89 removed outlier: 3.520A pdb=" N LEU C 86 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 123 " --> pdb=" O TRP C 68 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP C 68 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.824A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 85 through 89 removed outlier: 7.652A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 99 through 100 removed outlier: 5.324A pdb=" N TYR D 207 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU D 198 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU D 209 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D 196 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS D 211 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR D 213 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D 192 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE D 215 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 217 " --> pdb=" O GLU D 188 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1854 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: 3.35 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 207 1.03 - 1.23: 24 1.23 - 1.42: 5112 1.42 - 1.62: 6844 1.62 - 1.81: 48 Bond restraints: 12235 Sorted by residual: bond pdb=" CZ2 SRO B 501 " pdb=" CH2 SRO B 501 " ideal model delta sigma weight residual 1.386 1.520 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" CG SRO B 501 " pdb=" CD2 SRO B 501 " ideal model delta sigma weight residual 1.438 1.508 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C PRO A 143 " pdb=" O PRO A 143 " ideal model delta sigma weight residual 1.228 1.162 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" CD1 SRO B 501 " pdb=" NE1 SRO B 501 " ideal model delta sigma weight residual 1.377 1.314 0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" C ASN A 141 " pdb=" O ASN A 141 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.26e-02 6.30e+03 7.31e+00 ... (remaining 12230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 16664 2.49 - 4.99: 219 4.99 - 7.48: 12 7.48 - 9.97: 4 9.97 - 12.46: 2 Bond angle restraints: 16901 Sorted by residual: angle pdb=" CA PHE A 142 " pdb=" C PHE A 142 " pdb=" N PRO A 143 " ideal model delta sigma weight residual 118.23 124.81 -6.58 9.20e-01 1.18e+00 5.11e+01 angle pdb=" CA PHE A 142 " pdb=" C PHE A 142 " pdb=" O PHE A 142 " ideal model delta sigma weight residual 120.25 113.75 6.50 1.08e+00 8.57e-01 3.62e+01 angle pdb=" C PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 112.00 99.54 12.46 2.50e+00 1.60e-01 2.49e+01 angle pdb=" N TYR A 140 " pdb=" CA TYR A 140 " pdb=" C TYR A 140 " ideal model delta sigma weight residual 108.75 100.34 8.41 1.71e+00 3.42e-01 2.42e+01 angle pdb=" C TYR A 140 " pdb=" CA TYR A 140 " pdb=" CB TYR A 140 " ideal model delta sigma weight residual 109.68 118.35 -8.67 1.98e+00 2.55e-01 1.92e+01 ... (remaining 16896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6303 17.95 - 35.89: 612 35.89 - 53.84: 151 53.84 - 71.78: 25 71.78 - 89.73: 8 Dihedral angle restraints: 7099 sinusoidal: 2858 harmonic: 4241 Sorted by residual: dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 150.19 -57.19 1 1.00e+01 1.00e-02 4.40e+01 dihedral pdb=" C PRO A 143 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta harmonic sigma weight residual -120.70 -107.45 -13.25 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" CA VAL D 30 " pdb=" C VAL D 30 " pdb=" N ARG D 31 " pdb=" CA ARG D 31 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 7096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1629 0.058 - 0.116: 228 0.116 - 0.175: 51 0.175 - 0.233: 1 0.233 - 0.291: 1 Chirality restraints: 1910 Sorted by residual: chirality pdb=" CA ARG D 28 " pdb=" N ARG D 28 " pdb=" C ARG D 28 " pdb=" CB ARG D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL C 305 " pdb=" CA VAL C 305 " pdb=" CG1 VAL C 305 " pdb=" CG2 VAL C 305 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA LEU C 73 " pdb=" N LEU C 73 " pdb=" C LEU C 73 " pdb=" CB LEU C 73 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 1907 not shown) Planarity restraints: 2000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 280 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.48e+01 pdb=" N PRO A 281 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 28 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO D 29 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 144 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C PHE A 144 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE A 144 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 145 " -0.012 2.00e-02 2.50e+03 ... (remaining 1997 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.54: 389 2.54 - 3.05: 8647 3.05 - 3.57: 14473 3.57 - 4.08: 20413 4.08 - 4.60: 30367 Nonbonded interactions: 74289 Sorted by model distance: nonbonded pdb=" HD2 ARG C 65 " pdb="HH11 ARG C 65 " model vdw 2.024 2.270 nonbonded pdb="HG21 ILE A 44 " pdb="HD13 ILE A 44 " model vdw 2.056 2.440 nonbonded pdb=" HB3 TYR A 126 " pdb=" HE1 TRP B 156 " model vdw 2.077 2.270 nonbonded pdb=" HB2 TYR A 126 " pdb=" HE1 TRP B 156 " model vdw 2.104 2.270 nonbonded pdb=" OD2 ASP C 42 " pdb=" HE ARG C 65 " model vdw 2.143 2.450 ... (remaining 74284 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 12 through 23 or resid 26 through 28 or resid 32 through 3 \ 3 or resid 39 through 43 or (resid 44 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name CD1)) or resid 45 through 62 or (res \ id 63 and (name N or name CA or name C or name O or name CB or name CG or name C \ D1 or name CD2 or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or na \ me CH2)) or resid 64 or (resid 65 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or \ resid 66 through 68 or resid 71 through 82 or resid 85 through 96 or resid 100 \ through 106 or resid 112 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or resid 127 through 154 or resid 158 through 160 o \ r resid 164 through 179 or (resid 180 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2 or name CD1)) or resid 181 through 309 or re \ sid 315 through 331 or resid 422 through 462)) selection = (chain 'B' and (resid 12 through 23 or resid 26 through 28 or resid 32 through 3 \ 3 or resid 39 through 68 or resid 71 through 96 or resid 100 or (resid 101 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or resid 102 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or resid 158 through 160 or resid 1 \ 64 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or ( \ resid 207 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 208 \ or (resid 209 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 210 through 275 or resid 278 throu \ gh 309 or resid 315 through 331 or resid 422 through 462)) selection = (chain 'C' and (resid 12 through 23 or resid 26 through 62 or (resid 63 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name NE1 or name CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or re \ sid 64 or (resid 65 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 66 thro \ ugh 82 or resid 85 through 106 or resid 112 through 125 or (resid 126 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name CE1 or name CE2 or name CZ or name OH )) or resid 127 through 199 or resi \ d 207 through 275 or resid 278 through 309 or resid 315 through 331 or resid 422 \ through 462)) selection = (chain 'D' and (resid 12 through 28 or resid 32 through 33 or resid 39 through 6 \ 8 or resid 71 through 82 or resid 85 through 96 or resid 100 or (resid 101 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or resid 102 through 106 or resid 112 through 153 or (resid 154 and (name \ N or name CA or name C or name O or name CB or name OG1 or name CG2)) or resid 1 \ 58 through 160 or resid 164 through 198 or (resid 199 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or na \ me CE2 or name CZ )) or (resid 207 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ o \ r name OH )) or resid 208 or (resid 209 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 210 throu \ gh 275 or resid 278 through 309 or resid 315 through 331 or resid 422 through 46 \ 2)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.330 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 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 : 0.004 0.134 12031 Z= 0.208 Angle : 0.629 12.463 16444 Z= 0.348 Chirality : 0.044 0.291 1910 Planarity : 0.005 0.096 1997 Dihedral : 15.262 89.727 4272 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.63 % Favored : 95.08 % Rotamer: Outliers : 0.53 % Allowed : 16.05 % Favored : 83.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.41 % 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: 0.53 (0.24), residues: 1362 helix: 2.48 (0.22), residues: 532 sheet: -1.23 (0.27), residues: 343 loop : -0.77 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 459 HIS 0.006 0.001 HIS B 158 PHE 0.028 0.001 PHE A 144 TYR 0.030 0.001 TYR A 114 ARG 0.003 0.000 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.15617 ( 605) hydrogen bonds : angle 7.34638 ( 1854) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.76434 ( 6) covalent geometry : bond 0.00424 (12028) covalent geometry : angle 0.62934 (16438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 379 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 TYR cc_start: 0.7449 (t80) cc_final: 0.7158 (t80) REVERT: B 259 LEU cc_start: 0.7905 (tp) cc_final: 0.7677 (tp) REVERT: C 49 LEU cc_start: 0.8281 (mt) cc_final: 0.8067 (mt) outliers start: 7 outliers final: 3 residues processed: 382 average time/residue: 0.2236 time to fit residues: 123.7053 Evaluate side-chains 270 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 TYR Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 207 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN D 309 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065977 restraints weight = 50091.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067969 restraints weight = 26997.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.069225 restraints weight = 18359.283| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12031 Z= 0.167 Angle : 0.534 6.859 16444 Z= 0.283 Chirality : 0.040 0.156 1910 Planarity : 0.004 0.066 1997 Dihedral : 5.273 59.193 1548 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 35.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.01 % Allowed : 20.30 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.93 (0.24), residues: 1362 helix: 2.91 (0.21), residues: 544 sheet: -1.19 (0.27), residues: 335 loop : -0.68 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 320 HIS 0.005 0.001 HIS C 118 PHE 0.011 0.001 PHE D 233 TYR 0.016 0.001 TYR D 262 ARG 0.007 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 605) hydrogen bonds : angle 5.12290 ( 1854) SS BOND : bond 0.00369 ( 3) SS BOND : angle 0.79762 ( 6) covalent geometry : bond 0.00348 (12028) covalent geometry : angle 0.53344 (16438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 267 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 VAL cc_start: 0.9660 (t) cc_final: 0.9441 (p) REVERT: A 238 ASP cc_start: 0.9359 (t0) cc_final: 0.9157 (t0) REVERT: A 290 CYS cc_start: 0.8960 (m) cc_final: 0.8530 (t) REVERT: A 441 TYR cc_start: 0.9282 (t80) cc_final: 0.8918 (t80) REVERT: B 287 PHE cc_start: 0.9252 (m-80) cc_final: 0.8227 (m-80) REVERT: B 291 MET cc_start: 0.8228 (mmp) cc_final: 0.4867 (mmp) REVERT: C 17 ASP cc_start: 0.9600 (OUTLIER) cc_final: 0.9332 (m-30) REVERT: C 233 PHE cc_start: 0.9157 (t80) cc_final: 0.8938 (t80) REVERT: D 102 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8277 (mp0) REVERT: D 130 GLN cc_start: 0.8378 (mt0) cc_final: 0.7892 (mt0) REVERT: D 291 MET cc_start: 0.8162 (ttp) cc_final: 0.7534 (ttp) outliers start: 79 outliers final: 52 residues processed: 301 average time/residue: 0.2073 time to fit residues: 93.2883 Evaluate side-chains 301 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064882 restraints weight = 51120.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066911 restraints weight = 26745.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068220 restraints weight = 17962.596| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12031 Z= 0.190 Angle : 0.519 4.907 16444 Z= 0.275 Chirality : 0.039 0.159 1910 Planarity : 0.004 0.047 1997 Dihedral : 4.734 50.548 1544 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 43.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.08 % Allowed : 22.74 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.04 (0.24), residues: 1362 helix: 3.08 (0.21), residues: 544 sheet: -1.28 (0.26), residues: 345 loop : -0.58 (0.32), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 33 HIS 0.003 0.001 HIS B 119 PHE 0.012 0.001 PHE B 265 TYR 0.012 0.001 TYR B 262 ARG 0.010 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 605) hydrogen bonds : angle 4.67069 ( 1854) SS BOND : bond 0.00318 ( 3) SS BOND : angle 0.77803 ( 6) covalent geometry : bond 0.00382 (12028) covalent geometry : angle 0.51868 (16438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 251 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.9112 (t0) cc_final: 0.8861 (t0) REVERT: A 290 CYS cc_start: 0.8915 (m) cc_final: 0.8494 (t) REVERT: A 441 TYR cc_start: 0.9305 (t80) cc_final: 0.8939 (t80) REVERT: B 262 TYR cc_start: 0.8123 (t80) cc_final: 0.7306 (t80) REVERT: B 266 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 233 PHE cc_start: 0.9202 (t80) cc_final: 0.9001 (t80) REVERT: C 238 ASP cc_start: 0.9429 (t0) cc_final: 0.9226 (t0) REVERT: D 64 TYR cc_start: 0.8787 (t80) cc_final: 0.8520 (t80) REVERT: D 102 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 105 ASP cc_start: 0.8980 (t0) cc_final: 0.8607 (t0) REVERT: D 130 GLN cc_start: 0.8429 (mt0) cc_final: 0.8133 (mp10) REVERT: D 291 MET cc_start: 0.8320 (ttp) cc_final: 0.7726 (ttp) outliers start: 80 outliers final: 57 residues processed: 285 average time/residue: 0.2086 time to fit residues: 89.2931 Evaluate side-chains 293 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 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 = 0.3638 r_free = 0.3638 target = 0.082923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.065359 restraints weight = 50315.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067263 restraints weight = 26837.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068535 restraints weight = 18031.882| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12031 Z= 0.163 Angle : 0.497 9.348 16444 Z= 0.257 Chirality : 0.039 0.250 1910 Planarity : 0.003 0.037 1997 Dihedral : 4.496 45.046 1544 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 45.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.78 % Allowed : 23.95 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.21 (0.24), residues: 1362 helix: 3.28 (0.21), residues: 544 sheet: -1.18 (0.27), residues: 346 loop : -0.58 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.003 0.001 HIS B 119 PHE 0.011 0.001 PHE B 233 TYR 0.014 0.001 TYR B 262 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 605) hydrogen bonds : angle 4.33957 ( 1854) SS BOND : bond 0.00267 ( 3) SS BOND : angle 0.74365 ( 6) covalent geometry : bond 0.00335 (12028) covalent geometry : angle 0.49651 (16438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 246 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9626 (tt) cc_final: 0.9405 (pp) REVERT: A 290 CYS cc_start: 0.8704 (m) cc_final: 0.8377 (m) REVERT: B 262 TYR cc_start: 0.8241 (t80) cc_final: 0.7224 (t80) REVERT: B 266 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8373 (mp) REVERT: B 287 PHE cc_start: 0.9328 (m-80) cc_final: 0.8769 (m-80) REVERT: B 291 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.5570 (mmp) REVERT: C 238 ASP cc_start: 0.9411 (t0) cc_final: 0.9096 (t0) REVERT: D 102 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8383 (mm-30) REVERT: D 105 ASP cc_start: 0.9015 (t0) cc_final: 0.8656 (t0) REVERT: D 130 GLN cc_start: 0.8457 (mt0) cc_final: 0.8183 (mp10) outliers start: 76 outliers final: 62 residues processed: 280 average time/residue: 0.1982 time to fit residues: 84.4899 Evaluate side-chains 299 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 5 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 112 optimal weight: 0.0030 chunk 134 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 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 = 0.3645 r_free = 0.3645 target = 0.083545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066179 restraints weight = 50202.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068104 restraints weight = 27190.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.069372 restraints weight = 18350.428| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12031 Z= 0.153 Angle : 0.484 8.568 16444 Z= 0.250 Chirality : 0.039 0.247 1910 Planarity : 0.003 0.036 1997 Dihedral : 4.326 40.800 1544 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 48.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.16 % Allowed : 25.10 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.33 (0.24), residues: 1362 helix: 3.38 (0.21), residues: 545 sheet: -1.08 (0.27), residues: 341 loop : -0.57 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.002 0.001 HIS B 119 PHE 0.012 0.001 PHE A 233 TYR 0.013 0.001 TYR B 286 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 605) hydrogen bonds : angle 4.20757 ( 1854) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.67690 ( 6) covalent geometry : bond 0.00318 (12028) covalent geometry : angle 0.48420 (16438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 240 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9678 (tt) cc_final: 0.9400 (pp) REVERT: A 105 ASP cc_start: 0.9129 (t0) cc_final: 0.8878 (t0) REVERT: A 155 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7254 (t) REVERT: A 441 TYR cc_start: 0.9265 (t80) cc_final: 0.9002 (t80) REVERT: B 262 TYR cc_start: 0.8128 (t80) cc_final: 0.7038 (t80) REVERT: B 266 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 291 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.5608 (mmp) REVERT: C 17 ASP cc_start: 0.9628 (OUTLIER) cc_final: 0.9399 (p0) REVERT: C 108 LYS cc_start: 0.9298 (tptp) cc_final: 0.8974 (tptp) REVERT: C 238 ASP cc_start: 0.9371 (t0) cc_final: 0.9035 (t0) REVERT: C 263 SER cc_start: 0.9726 (OUTLIER) cc_final: 0.9435 (p) REVERT: D 102 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8364 (mm-30) REVERT: D 130 GLN cc_start: 0.8434 (mt0) cc_final: 0.8152 (mp10) REVERT: D 291 MET cc_start: 0.8243 (ttp) cc_final: 0.7711 (ttp) outliers start: 81 outliers final: 64 residues processed: 281 average time/residue: 0.2291 time to fit residues: 98.6252 Evaluate side-chains 301 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 462 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 20 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 0.0270 chunk 123 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064687 restraints weight = 51437.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066605 restraints weight = 27325.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067863 restraints weight = 18364.673| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12031 Z= 0.137 Angle : 0.472 8.827 16444 Z= 0.243 Chirality : 0.039 0.210 1910 Planarity : 0.003 0.035 1997 Dihedral : 4.222 39.585 1544 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 49.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.86 % Allowed : 26.24 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.45 (0.24), residues: 1362 helix: 3.51 (0.21), residues: 544 sheet: -1.04 (0.27), residues: 346 loop : -0.48 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.002 0.001 HIS C 323 PHE 0.009 0.001 PHE A 233 TYR 0.014 0.001 TYR A 286 ARG 0.007 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 605) hydrogen bonds : angle 4.09628 ( 1854) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.68242 ( 6) covalent geometry : bond 0.00287 (12028) covalent geometry : angle 0.47181 (16438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 238 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9689 (tt) cc_final: 0.9413 (pp) REVERT: A 105 ASP cc_start: 0.9145 (t0) cc_final: 0.8891 (t0) REVERT: A 155 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7142 (t) REVERT: B 158 HIS cc_start: 0.8725 (m170) cc_final: 0.8257 (m-70) REVERT: B 262 TYR cc_start: 0.8207 (t80) cc_final: 0.7112 (t80) REVERT: B 266 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.8245 (mp) REVERT: B 287 PHE cc_start: 0.9334 (m-80) cc_final: 0.8748 (m-80) REVERT: B 291 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.5372 (mmp) REVERT: C 17 ASP cc_start: 0.9658 (OUTLIER) cc_final: 0.9414 (p0) REVERT: C 238 ASP cc_start: 0.9396 (t0) cc_final: 0.9029 (t0) REVERT: C 263 SER cc_start: 0.9727 (OUTLIER) cc_final: 0.9442 (p) REVERT: D 56 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8836 (mm-40) REVERT: D 102 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 129 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8899 (pp) REVERT: D 130 GLN cc_start: 0.8425 (mt0) cc_final: 0.8149 (mp10) REVERT: D 147 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7245 (mm110) REVERT: D 291 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7821 (ttp) outliers start: 77 outliers final: 61 residues processed: 275 average time/residue: 0.1927 time to fit residues: 80.3183 Evaluate side-chains 297 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 434 ASP Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 37 optimal weight: 0.0030 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 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 = 0.3611 r_free = 0.3611 target = 0.082938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065143 restraints weight = 51078.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067136 restraints weight = 27393.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.068371 restraints weight = 18323.361| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12031 Z= 0.127 Angle : 0.470 10.020 16444 Z= 0.240 Chirality : 0.039 0.213 1910 Planarity : 0.003 0.038 1997 Dihedral : 4.151 39.959 1544 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 49.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.08 % Allowed : 26.31 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.58 (0.24), residues: 1362 helix: 3.59 (0.21), residues: 544 sheet: -0.98 (0.27), residues: 346 loop : -0.39 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.002 0.001 HIS C 323 PHE 0.009 0.001 PHE A 303 TYR 0.016 0.001 TYR A 286 ARG 0.004 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02678 ( 605) hydrogen bonds : angle 4.00407 ( 1854) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.63928 ( 6) covalent geometry : bond 0.00266 (12028) covalent geometry : angle 0.46952 (16438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 232 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9667 (tt) cc_final: 0.9410 (pp) REVERT: A 105 ASP cc_start: 0.9130 (t0) cc_final: 0.8872 (t0) REVERT: A 155 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7213 (t) REVERT: B 158 HIS cc_start: 0.8717 (m170) cc_final: 0.8260 (m-70) REVERT: B 262 TYR cc_start: 0.8151 (t80) cc_final: 0.7148 (t80) REVERT: B 266 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 287 PHE cc_start: 0.9357 (m-80) cc_final: 0.8851 (m-80) REVERT: B 291 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.5215 (mmp) REVERT: C 233 PHE cc_start: 0.8957 (t80) cc_final: 0.8750 (t80) REVERT: C 238 ASP cc_start: 0.9358 (t0) cc_final: 0.8979 (t0) REVERT: C 263 SER cc_start: 0.9718 (OUTLIER) cc_final: 0.9438 (p) REVERT: D 56 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8857 (mm110) REVERT: D 129 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8765 (pp) REVERT: D 130 GLN cc_start: 0.8471 (mt0) cc_final: 0.8196 (mp10) REVERT: D 147 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7171 (mm110) REVERT: D 291 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7750 (ttp) outliers start: 80 outliers final: 69 residues processed: 266 average time/residue: 0.1985 time to fit residues: 79.8736 Evaluate side-chains 306 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 36 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 0.0070 chunk 79 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 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 = 0.3623 r_free = 0.3623 target = 0.083165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065198 restraints weight = 51226.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067147 restraints weight = 27316.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068420 restraints weight = 18493.529| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12031 Z= 0.106 Angle : 0.471 9.788 16444 Z= 0.236 Chirality : 0.039 0.249 1910 Planarity : 0.003 0.036 1997 Dihedral : 4.063 39.409 1544 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.10 % Allowed : 27.60 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.70 (0.24), residues: 1362 helix: 3.72 (0.20), residues: 543 sheet: -0.89 (0.28), residues: 344 loop : -0.38 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 459 HIS 0.002 0.000 HIS C 323 PHE 0.010 0.001 PHE A 303 TYR 0.016 0.001 TYR A 286 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02555 ( 605) hydrogen bonds : angle 3.90536 ( 1854) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.59346 ( 6) covalent geometry : bond 0.00231 (12028) covalent geometry : angle 0.47048 (16438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9643 (tt) cc_final: 0.9405 (pp) REVERT: A 105 ASP cc_start: 0.9108 (t0) cc_final: 0.8840 (t70) REVERT: A 155 SER cc_start: 0.7767 (OUTLIER) cc_final: 0.7170 (t) REVERT: B 158 HIS cc_start: 0.8696 (m170) cc_final: 0.8319 (m-70) REVERT: B 262 TYR cc_start: 0.8146 (t80) cc_final: 0.7168 (t80) REVERT: B 266 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 287 PHE cc_start: 0.9365 (m-80) cc_final: 0.8882 (m-80) REVERT: B 291 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.5180 (mmp) REVERT: C 17 ASP cc_start: 0.9637 (OUTLIER) cc_final: 0.9356 (m-30) REVERT: C 186 GLU cc_start: 0.8454 (tt0) cc_final: 0.8237 (tt0) REVERT: C 238 ASP cc_start: 0.9350 (t0) cc_final: 0.8958 (t0) REVERT: C 263 SER cc_start: 0.9703 (OUTLIER) cc_final: 0.9430 (p) REVERT: D 56 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8865 (mm110) REVERT: D 129 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8727 (pp) REVERT: D 130 GLN cc_start: 0.8527 (mt0) cc_final: 0.8244 (mp10) REVERT: D 147 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7151 (mm110) REVERT: D 291 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7822 (ttp) outliers start: 67 outliers final: 57 residues processed: 267 average time/residue: 0.1902 time to fit residues: 77.1973 Evaluate side-chains 292 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 24 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 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 = 0.3626 r_free = 0.3626 target = 0.083514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064851 restraints weight = 51622.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066782 restraints weight = 28009.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067997 restraints weight = 19122.371| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12031 Z= 0.161 Angle : 0.508 9.206 16444 Z= 0.256 Chirality : 0.039 0.256 1910 Planarity : 0.003 0.032 1997 Dihedral : 4.168 42.427 1544 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 53.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.70 % Allowed : 27.53 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.58 (0.24), residues: 1362 helix: 3.60 (0.20), residues: 544 sheet: -0.94 (0.28), residues: 338 loop : -0.44 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 459 HIS 0.003 0.001 HIS B 119 PHE 0.010 0.001 PHE B 265 TYR 0.018 0.001 TYR A 286 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02712 ( 605) hydrogen bonds : angle 4.05219 ( 1854) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.77061 ( 6) covalent geometry : bond 0.00335 (12028) covalent geometry : angle 0.50776 (16438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 227 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9651 (tt) cc_final: 0.9392 (pp) REVERT: A 105 ASP cc_start: 0.9121 (t0) cc_final: 0.8850 (t0) REVERT: A 155 SER cc_start: 0.7777 (OUTLIER) cc_final: 0.7188 (t) REVERT: A 263 SER cc_start: 0.9725 (m) cc_final: 0.9470 (p) REVERT: B 158 HIS cc_start: 0.8738 (m170) cc_final: 0.8294 (m-70) REVERT: B 262 TYR cc_start: 0.8153 (t80) cc_final: 0.7221 (t80) REVERT: B 266 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 153 PHE cc_start: 0.9441 (m-80) cc_final: 0.9053 (m-80) REVERT: C 186 GLU cc_start: 0.8462 (tt0) cc_final: 0.8231 (tt0) REVERT: C 238 ASP cc_start: 0.9330 (t0) cc_final: 0.8934 (t0) REVERT: C 263 SER cc_start: 0.9732 (OUTLIER) cc_final: 0.9467 (p) REVERT: D 56 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8899 (mm110) REVERT: D 129 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8689 (pp) REVERT: D 130 GLN cc_start: 0.8465 (mt0) cc_final: 0.8204 (mp10) REVERT: D 286 TYR cc_start: 0.8861 (m-80) cc_final: 0.8445 (m-10) outliers start: 75 outliers final: 66 residues processed: 264 average time/residue: 0.1895 time to fit residues: 76.9592 Evaluate side-chains 296 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 226 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 462 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 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 = 0.3611 r_free = 0.3611 target = 0.084302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067422 restraints weight = 46270.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069305 restraints weight = 26544.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.070469 restraints weight = 18851.408| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12031 Z= 0.125 Angle : 0.493 9.665 16444 Z= 0.246 Chirality : 0.040 0.262 1910 Planarity : 0.003 0.032 1997 Dihedral : 4.131 42.239 1544 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 52.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.55 % Allowed : 27.68 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.64 (0.24), residues: 1362 helix: 3.66 (0.20), residues: 543 sheet: -0.91 (0.28), residues: 344 loop : -0.41 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 459 HIS 0.002 0.000 HIS C 323 PHE 0.011 0.001 PHE A 303 TYR 0.018 0.001 TYR A 286 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02650 ( 605) hydrogen bonds : angle 3.97004 ( 1854) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.70234 ( 6) covalent geometry : bond 0.00267 (12028) covalent geometry : angle 0.49256 (16438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 227 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.9641 (tt) cc_final: 0.9375 (pp) REVERT: A 105 ASP cc_start: 0.9171 (t0) cc_final: 0.8915 (t70) REVERT: A 155 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7284 (t) REVERT: A 263 SER cc_start: 0.9682 (m) cc_final: 0.9436 (p) REVERT: B 158 HIS cc_start: 0.8816 (m170) cc_final: 0.8333 (m-70) REVERT: B 262 TYR cc_start: 0.8197 (t80) cc_final: 0.7308 (t80) REVERT: B 266 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8420 (mp) REVERT: C 153 PHE cc_start: 0.9423 (m-80) cc_final: 0.9062 (m-80) REVERT: C 186 GLU cc_start: 0.8542 (tt0) cc_final: 0.8295 (tt0) REVERT: C 238 ASP cc_start: 0.9435 (t0) cc_final: 0.9037 (t0) REVERT: C 263 SER cc_start: 0.9739 (OUTLIER) cc_final: 0.9457 (p) REVERT: D 56 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8820 (mm110) REVERT: D 129 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8710 (pp) REVERT: D 130 GLN cc_start: 0.8487 (mt0) cc_final: 0.8197 (mp10) REVERT: D 286 TYR cc_start: 0.8832 (m-80) cc_final: 0.8432 (m-10) outliers start: 73 outliers final: 66 residues processed: 261 average time/residue: 0.1947 time to fit residues: 78.1850 Evaluate side-chains 295 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 225 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 18 HIS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 462 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 13 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 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 = 0.3609 r_free = 0.3609 target = 0.082794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.064017 restraints weight = 52217.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065917 restraints weight = 28178.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.067145 restraints weight = 19217.731| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12031 Z= 0.183 Angle : 0.535 9.131 16444 Z= 0.270 Chirality : 0.040 0.254 1910 Planarity : 0.003 0.033 1997 Dihedral : 4.284 45.476 1544 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 56.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 6.01 % Allowed : 27.30 % Favored : 66.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.46 (0.24), residues: 1362 helix: 3.48 (0.20), residues: 546 sheet: -0.98 (0.28), residues: 343 loop : -0.51 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 459 HIS 0.006 0.001 HIS C 18 PHE 0.012 0.001 PHE C 233 TYR 0.023 0.001 TYR A 286 ARG 0.002 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.02830 ( 605) hydrogen bonds : angle 4.14688 ( 1854) SS BOND : bond 0.00301 ( 3) SS BOND : angle 0.90010 ( 6) covalent geometry : bond 0.00378 (12028) covalent geometry : angle 0.53504 (16438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.66 seconds wall clock time: 73 minutes 15.56 seconds (4395.56 seconds total)