Starting phenix.real_space_refine on Mon Dec 30 01:47:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c20_16386/12_2024/8c20_16386_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c20_16386/12_2024/8c20_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_16386/12_2024/8c20_16386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c20_16386/12_2024/8c20_16386.map" model { file = "/net/cci-nas-00/data/ceres_data/8c20_16386/12_2024/8c20_16386_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c20_16386/12_2024/8c20_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.99, per 1000 atoms: 0.67 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: 3.04 Conformation dependent library (CDL) restraints added in 1.6 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: 1.31 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: 3.75 Time building geometry restraints manager: 3.53 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: 2.060 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: 0.340 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.840 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- 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 12028 Z= 0.278 Angle : 0.629 12.463 16438 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 *********************** 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 : 1.867 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: 0.2318 time to fit residues: 128.0581 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 : 1.491 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 12028 Z= 0.224 Angle : 0.533 6.859 16438 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 : 35.53 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 *********************** 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 : 1.418 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 441 TYR cc_start: 0.7359 (t80) cc_final: 0.7092 (t80) REVERT: B 287 PHE cc_start: 0.6849 (m-80) cc_final: 0.6475 (m-80) REVERT: B 291 MET cc_start: 0.5404 (mmp) cc_final: 0.3215 (mmp) REVERT: C 178 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7525 (pptt) outliers start: 79 outliers final: 52 residues processed: 301 average time/residue: 0.2127 time to fit residues: 95.5953 Evaluate side-chains 298 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 178 LYS 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 70 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 0.4980 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12028 Z= 0.135 Angle : 0.464 6.189 16438 Z= 0.245 Chirality : 0.040 0.188 1910 Planarity : 0.004 0.046 1997 Dihedral : 4.628 49.822 1544 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 37.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.57 % Allowed : 23.12 % Favored : 73.31 % 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: 1.20 (0.24), residues: 1362 helix: 3.19 (0.21), residues: 543 sheet: -1.16 (0.27), residues: 340 loop : -0.49 (0.32), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.008 0.001 PHE A 233 TYR 0.014 0.001 TYR A 286 ARG 0.013 0.000 ARG D 34 *********************** 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 312 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 1.455 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: B 266 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6935 (mp) REVERT: B 287 PHE cc_start: 0.6890 (m-80) cc_final: 0.6511 (m-80) REVERT: B 291 MET cc_start: 0.5641 (mmp) cc_final: 0.4510 (mmp) REVERT: C 178 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7482 (pptt) REVERT: D 105 ASP cc_start: 0.6083 (t0) cc_final: 0.5792 (t0) outliers start: 47 outliers final: 34 residues processed: 282 average time/residue: 0.2187 time to fit residues: 91.8400 Evaluate side-chains 288 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 192 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 295 VAL 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 233 PHE 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 440 ILE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 178 LYS 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 266 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 437 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 126 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** 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 D 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12028 Z= 0.115 Angle : 0.454 9.077 16438 Z= 0.235 Chirality : 0.040 0.253 1910 Planarity : 0.003 0.034 1997 Dihedral : 4.269 42.757 1542 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 38.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.35 % Allowed : 24.71 % Favored : 71.94 % 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: 3.36 (0.21), residues: 544 sheet: -0.93 (0.28), residues: 333 loop : -0.41 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.013 0.001 PHE A 233 TYR 0.021 0.001 TYR B 262 ARG 0.002 0.000 ARG A 251 *********************** 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 306 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.504 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: C 178 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7446 (pptt) outliers start: 44 outliers final: 34 residues processed: 279 average time/residue: 0.2163 time to fit residues: 89.9716 Evaluate side-chains 284 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 116 TYR 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 295 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 178 LYS 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 260 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.0470 chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 0.0980 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.4282 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12028 Z= 0.250 Angle : 0.514 7.457 16438 Z= 0.266 Chirality : 0.039 0.255 1910 Planarity : 0.003 0.033 1997 Dihedral : 4.275 43.207 1542 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 47.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.86 % Allowed : 24.03 % Favored : 70.11 % 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: 1.42 (0.24), residues: 1362 helix: 3.39 (0.21), residues: 545 sheet: -1.00 (0.28), residues: 336 loop : -0.47 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.003 0.001 HIS B 119 PHE 0.012 0.001 PHE A 303 TYR 0.020 0.001 TYR A 262 ARG 0.004 0.000 ARG A 251 *********************** 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 316 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 1.400 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: B 291 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5375 (mmp) REVERT: C 178 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7584 (pptt) outliers start: 77 outliers final: 56 residues processed: 273 average time/residue: 0.2187 time to fit residues: 89.6246 Evaluate side-chains 291 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 233 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 192 VAL 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 A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE 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 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 440 ILE 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU 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 295 VAL Chi-restraints excluded: chain C residue 433 LEU 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 D residue 62 ILE Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 214 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12028 Z= 0.147 Angle : 0.462 9.401 16438 Z= 0.237 Chirality : 0.039 0.252 1910 Planarity : 0.003 0.033 1997 Dihedral : 4.083 39.280 1542 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 45.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.73 % Allowed : 27.07 % Favored : 69.20 % 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: 1.53 (0.24), residues: 1362 helix: 3.51 (0.21), residues: 551 sheet: -0.91 (0.27), residues: 341 loop : -0.52 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.009 0.001 PHE D 303 TYR 0.013 0.001 TYR B 286 ARG 0.004 0.000 ARG A 251 *********************** 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 290 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 241 time to evaluate : 1.354 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: B 291 MET cc_start: 0.5426 (mmp) cc_final: 0.4434 (mmp) REVERT: C 178 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7565 (pptt) REVERT: D 45 MET cc_start: 0.6314 (tpp) cc_final: 0.5964 (tpt) outliers start: 49 outliers final: 40 residues processed: 266 average time/residue: 0.2105 time to fit residues: 83.8646 Evaluate side-chains 274 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 192 VAL 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 295 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU 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 267 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 443 LEU 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 214 VAL Chi-restraints excluded: chain D residue 266 LEU 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 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 0.0030 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 82 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12028 Z= 0.117 Angle : 0.452 10.344 16438 Z= 0.229 Chirality : 0.039 0.254 1910 Planarity : 0.003 0.031 1997 Dihedral : 3.873 34.523 1542 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 44.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.50 % Allowed : 27.38 % Favored : 69.13 % 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: 1.76 (0.24), residues: 1362 helix: 3.69 (0.21), residues: 544 sheet: -0.80 (0.28), residues: 343 loop : -0.30 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.013 0.001 PHE A 233 TYR 0.013 0.001 TYR B 286 ARG 0.003 0.000 ARG A 251 *********************** 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 295 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.592 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 155 SER cc_start: 0.7427 (OUTLIER) cc_final: 0.7184 (t) REVERT: B 262 TYR cc_start: 0.5556 (t80) cc_final: 0.4994 (t80) REVERT: B 291 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.4725 (mmp) REVERT: C 178 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7572 (pptt) REVERT: C 443 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7921 (tp) REVERT: D 45 MET cc_start: 0.6186 (tpp) cc_final: 0.5950 (tpt) outliers start: 46 outliers final: 38 residues processed: 272 average time/residue: 0.2148 time to fit residues: 86.6137 Evaluate side-chains 276 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 155 SER Chi-restraints excluded: chain A residue 192 VAL 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 237 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 291 MET 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 216 ILE 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 295 VAL Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 252 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 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 53 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 105 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12028 Z= 0.342 Angle : 0.596 7.646 16438 Z= 0.306 Chirality : 0.040 0.231 1910 Planarity : 0.004 0.062 1997 Dihedral : 4.316 42.608 1542 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 57.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.40 % Allowed : 26.46 % Favored : 68.14 % 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: 1.22 (0.24), residues: 1362 helix: 3.17 (0.20), residues: 546 sheet: -1.02 (0.28), residues: 343 loop : -0.56 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 68 HIS 0.004 0.001 HIS B 119 PHE 0.016 0.002 PHE B 265 TYR 0.016 0.002 TYR A 286 ARG 0.022 0.001 ARG A 328 *********************** 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 283 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 TYR cc_start: 0.5538 (t80) cc_final: 0.5333 (t80) REVERT: B 291 MET cc_start: 0.5491 (OUTLIER) cc_final: 0.3954 (mmp) REVERT: C 178 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7733 (pptt) outliers start: 71 outliers final: 62 residues processed: 246 average time/residue: 0.2044 time to fit residues: 76.6262 Evaluate side-chains 274 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 210 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 192 VAL 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 259 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE 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 258 LEU Chi-restraints excluded: chain B residue 271 ASP 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 49 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 ILE 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 216 ILE 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 263 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 293 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 D residue 41 ILE Chi-restraints excluded: chain D residue 57 VAL 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 214 VAL 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 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 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 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12028 Z= 0.133 Angle : 0.478 10.462 16438 Z= 0.242 Chirality : 0.040 0.261 1910 Planarity : 0.003 0.035 1997 Dihedral : 4.032 39.514 1542 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 48.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.80 % Allowed : 28.37 % Favored : 67.83 % 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: 1.61 (0.24), residues: 1362 helix: 3.53 (0.20), residues: 546 sheet: -0.88 (0.28), residues: 341 loop : -0.36 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.013 0.001 PHE C 233 TYR 0.015 0.001 TYR A 286 ARG 0.003 0.000 ARG A 251 *********************** 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 283 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.6328 (t80) REVERT: B 291 MET cc_start: 0.5273 (OUTLIER) cc_final: 0.4014 (mmp) REVERT: C 178 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7660 (pptt) outliers start: 50 outliers final: 42 residues processed: 255 average time/residue: 0.2224 time to fit residues: 86.2994 Evaluate side-chains 273 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 192 VAL 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 262 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU 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 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU 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 225 VAL Chi-restraints excluded: chain D residue 252 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 127 optimal weight: 0.4980 chunk 110 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12028 Z= 0.131 Angle : 0.489 10.395 16438 Z= 0.245 Chirality : 0.040 0.259 1910 Planarity : 0.003 0.038 1997 Dihedral : 3.926 38.414 1542 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 50.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.50 % Allowed : 28.90 % 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: 1.69 (0.24), residues: 1362 helix: 3.57 (0.20), residues: 545 sheet: -0.82 (0.28), residues: 343 loop : -0.29 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.032 0.001 PHE D 303 TYR 0.014 0.001 TYR A 286 ARG 0.003 0.000 ARG A 251 ********************** 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 279 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 233 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 TYR cc_start: 0.5724 (t80) cc_final: 0.5256 (t80) REVERT: C 178 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7677 (pptt) REVERT: D 104 VAL cc_start: 0.8526 (t) cc_final: 0.8234 (t) outliers start: 46 outliers final: 41 residues processed: 253 average time/residue: 0.2031 time to fit residues: 77.6575 Evaluate side-chains 270 residues out of total 1315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 192 VAL 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 295 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 258 LEU 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 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 178 LYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 443 LEU 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 225 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 252 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 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.084110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066329 restraints weight = 50112.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068348 restraints weight = 26867.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.069710 restraints weight = 18007.262| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12028 Z= 0.133 Angle : 0.498 10.438 16438 Z= 0.251 Chirality : 0.040 0.263 1910 Planarity : 0.003 0.039 1997 Dihedral : 3.885 37.660 1542 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 50.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.57 % Allowed : 29.20 % Favored : 67.22 % 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: 1.73 (0.24), residues: 1362 helix: 3.61 (0.21), residues: 544 sheet: -0.81 (0.28), residues: 348 loop : -0.24 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 459 HIS 0.002 0.000 HIS C 323 PHE 0.029 0.001 PHE D 303 TYR 0.016 0.001 TYR A 286 ARG 0.003 0.000 ARG A 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2764.87 seconds wall clock time: 51 minutes 39.23 seconds (3099.23 seconds total)