Starting phenix.real_space_refine on Fri Jun 13 22:34:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfw_45565/06_2025/9cfw_45565.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.048 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 95 5.16 5 C 9983 2.51 5 N 2714 2.21 5 O 3035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15838 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "C" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "D" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2896 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "P" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5874 Classifications: {'peptide': 720} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 693} Chain: "R" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.22, per 1000 atoms: 0.65 Number of scatterers: 15838 At special positions: 0 Unit cell: (188.44, 125.178, 138.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 8 15.00 Mg 3 11.99 O 3035 8.00 N 2714 7.00 C 9983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 2.1 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 26 sheets defined 54.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.867A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.153A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.703A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.731A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 4.095A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 286 through 296 removed outlier: 4.048A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.595A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 353 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.743A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.962A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.644A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.774A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.690A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.777A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.564A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.556A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.807A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.288A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.507A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.670A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 214 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.766A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.347A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'P' and resid 1 through 8 removed outlier: 3.814A pdb=" N ALA P 4 " --> pdb=" O MET P 1 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR P 6 " --> pdb=" O SER P 3 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG P 8 " --> pdb=" O LEU P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 19 Processing helix chain 'P' and resid 24 through 38 Processing helix chain 'P' and resid 58 through 61 removed outlier: 3.802A pdb=" N TYR P 61 " --> pdb=" O LEU P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 70 Processing helix chain 'P' and resid 80 through 96 removed outlier: 3.834A pdb=" N VAL P 84 " --> pdb=" O HIS P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 128 through 142 Processing helix chain 'P' and resid 142 through 150 Processing helix chain 'P' and resid 189 through 194 removed outlier: 4.178A pdb=" N VAL P 193 " --> pdb=" O LYS P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 removed outlier: 4.394A pdb=" N TYR P 206 " --> pdb=" O PHE P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 218 Processing helix chain 'P' and resid 225 through 228 Processing helix chain 'P' and resid 229 through 234 removed outlier: 4.278A pdb=" N LYS P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 244 through 259 Processing helix chain 'P' and resid 262 through 281 Processing helix chain 'P' and resid 296 through 307 removed outlier: 4.713A pdb=" N LEU P 300 " --> pdb=" O THR P 296 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR P 302 " --> pdb=" O ASN P 298 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG P 305 " --> pdb=" O LYS P 301 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 318 removed outlier: 3.750A pdb=" N GLU P 316 " --> pdb=" O THR P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 367 removed outlier: 3.654A pdb=" N ILE P 362 " --> pdb=" O LEU P 358 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA P 367 " --> pdb=" O ASN P 363 " (cutoff:3.500A) Processing helix chain 'P' and resid 397 through 429 removed outlier: 3.589A pdb=" N GLU P 416 " --> pdb=" O GLN P 412 " (cutoff:3.500A) Processing helix chain 'P' and resid 441 through 450 removed outlier: 3.742A pdb=" N ASP P 446 " --> pdb=" O LYS P 442 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU P 447 " --> pdb=" O ILE P 443 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 460 Processing helix chain 'P' and resid 470 through 482 Processing helix chain 'P' and resid 497 through 502 removed outlier: 4.035A pdb=" N LEU P 502 " --> pdb=" O ARG P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 528 removed outlier: 3.874A pdb=" N ASN P 528 " --> pdb=" O LEU P 524 " (cutoff:3.500A) Processing helix chain 'P' and resid 532 through 541 removed outlier: 3.670A pdb=" N LYS P 536 " --> pdb=" O PHE P 532 " (cutoff:3.500A) Processing helix chain 'P' and resid 544 through 551 Processing helix chain 'P' and resid 554 through 558 Processing helix chain 'P' and resid 564 through 582 Processing helix chain 'P' and resid 603 through 614 Processing helix chain 'P' and resid 615 through 625 Processing helix chain 'P' and resid 633 through 641 Processing helix chain 'P' and resid 642 through 648 Proline residue: P 645 - end of helix Processing helix chain 'P' and resid 654 through 666 Processing helix chain 'P' and resid 685 through 718 removed outlier: 4.113A pdb=" N GLN P 700 " --> pdb=" O GLU P 696 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER P 701 " --> pdb=" O VAL P 697 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG P 716 " --> pdb=" O GLY P 712 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 4.288A pdb=" N GLU R 12 " --> pdb=" O GLU R 8 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU R 19 " --> pdb=" O GLU R 15 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE R 20 " --> pdb=" O ALA R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 removed outlier: 3.795A pdb=" N THR R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 54 Processing helix chain 'R' and resid 65 through 77 Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'R' and resid 103 through 113 removed outlier: 3.721A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 130 removed outlier: 4.088A pdb=" N GLU R 128 " --> pdb=" O GLU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.874A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.599A pdb=" N LYS B 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.458A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.892A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.659A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.928A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.568A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'P' and resid 43 through 45 removed outlier: 6.562A pdb=" N ALA P 100 " --> pdb=" O ALA P 586 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE P 588 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET P 102 " --> pdb=" O ILE P 588 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS P 590 " --> pdb=" O MET P 102 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER P 104 " --> pdb=" O CYS P 590 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET P 167 " --> pdb=" O LEU P 384 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY P 164 " --> pdb=" O SER P 184 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER P 184 " --> pdb=" O GLY P 164 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR P 166 " --> pdb=" O ILE P 182 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE P 182 " --> pdb=" O TYR P 166 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP P 168 " --> pdb=" O GLY P 180 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY P 180 " --> pdb=" O ASP P 168 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN P 170 " --> pdb=" O VAL P 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AC3, first strand: chain 'P' and resid 284 through 286 Processing sheet with id=AC4, first strand: chain 'P' and resid 320 through 325 Processing sheet with id=AC5, first strand: chain 'P' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'P' and resid 629 through 632 removed outlier: 3.635A pdb=" N TYR P 629 " --> pdb=" O ILE P 682 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 28 through 29 Processing sheet with id=AC8, first strand: chain 'R' and resid 100 through 102 791 hydrogen bonds defined for protein. 2112 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: 6.10 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4023 1.33 - 1.45: 3111 1.45 - 1.58: 8862 1.58 - 1.70: 4 1.70 - 1.82: 165 Bond restraints: 16165 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.343 0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.346 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C4 ADP P 801 " pdb=" C5 ADP P 801 " ideal model delta sigma weight residual 1.490 1.349 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 16160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 21230 4.02 - 8.04: 621 8.04 - 12.06: 23 12.06 - 16.08: 2 16.08 - 20.10: 1 Bond angle restraints: 21877 Sorted by residual: angle pdb=" O1B ADP C 401 " pdb=" PB ADP C 401 " pdb=" O2B ADP C 401 " ideal model delta sigma weight residual 119.90 99.80 20.10 3.00e+00 1.11e-01 4.49e+01 angle pdb=" C LEU R 113 " pdb=" N GLY R 114 " pdb=" CA GLY R 114 " ideal model delta sigma weight residual 120.10 125.52 -5.42 9.50e-01 1.11e+00 3.25e+01 angle pdb=" CA ASP R 65 " pdb=" CB ASP R 65 " pdb=" CG ASP R 65 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" CA ASN P 441 " pdb=" CB ASN P 441 " pdb=" CG ASN P 441 " ideal model delta sigma weight residual 112.60 117.86 -5.26 1.00e+00 1.00e+00 2.77e+01 angle pdb=" C ILE C 71 " pdb=" N GLU C 72 " pdb=" CA GLU C 72 " ideal model delta sigma weight residual 122.84 129.59 -6.75 1.30e+00 5.92e-01 2.70e+01 ... (remaining 21872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 9518 33.89 - 67.78: 221 67.78 - 101.66: 29 101.66 - 135.55: 4 135.55 - 169.44: 1 Dihedral angle restraints: 9773 sinusoidal: 4022 harmonic: 5751 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.43 -169.44 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 63.91 -123.92 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 61.45 -121.45 1 2.00e+01 2.50e-03 3.65e+01 ... (remaining 9770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1586 0.085 - 0.170: 663 0.170 - 0.255: 132 0.255 - 0.340: 22 0.340 - 0.424: 3 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CA GLU R 115 " pdb=" N GLU R 115 " pdb=" C GLU R 115 " pdb=" CB GLU R 115 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CB THR R 45 " pdb=" CA THR R 45 " pdb=" OG1 THR R 45 " pdb=" CG2 THR R 45 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB ILE R 64 " pdb=" CA ILE R 64 " pdb=" CG1 ILE R 64 " pdb=" CG2 ILE R 64 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2403 not shown) Planarity restraints: 2821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " -0.236 2.00e-02 2.50e+03 1.19e-01 3.57e+02 pdb=" CG TRP B 340 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " 0.136 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " -0.154 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.089 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B 401 " 0.258 2.00e-02 2.50e+03 1.09e-01 3.26e+02 pdb=" C2 ADP B 401 " -0.053 2.00e-02 2.50e+03 pdb=" C4 ADP B 401 " -0.077 2.00e-02 2.50e+03 pdb=" C5 ADP B 401 " -0.053 2.00e-02 2.50e+03 pdb=" C6 ADP B 401 " 0.017 2.00e-02 2.50e+03 pdb=" C8 ADP B 401 " -0.089 2.00e-02 2.50e+03 pdb=" N1 ADP B 401 " 0.024 2.00e-02 2.50e+03 pdb=" N3 ADP B 401 " -0.073 2.00e-02 2.50e+03 pdb=" N6 ADP B 401 " 0.173 2.00e-02 2.50e+03 pdb=" N7 ADP B 401 " -0.067 2.00e-02 2.50e+03 pdb=" N9 ADP B 401 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.181 2.00e-02 2.50e+03 9.25e-02 2.14e+02 pdb=" CG TRP D 340 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.115 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.098 2.00e-02 2.50e+03 ... (remaining 2818 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 12 2.44 - 3.05: 9575 3.05 - 3.67: 23725 3.67 - 4.28: 36942 4.28 - 4.90: 61379 Nonbonded interactions: 131633 Sorted by model distance: nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 1.823 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.848 2.170 nonbonded pdb=" O1A ADP B 401 " pdb="MG MG B 402 " model vdw 1.895 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.906 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 1.923 2.170 ... (remaining 131628 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.380 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.780 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 : 0.013 0.147 16165 Z= 0.764 Angle : 1.833 20.099 21877 Z= 1.204 Chirality : 0.092 0.424 2406 Planarity : 0.017 0.178 2821 Dihedral : 14.921 169.437 6077 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 1.88 % Allowed : 4.41 % Favored : 93.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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 (0.17), residues: 1971 helix: -1.89 (0.14), residues: 896 sheet: -0.76 (0.36), residues: 178 loop : -0.07 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.236 0.029 TRP B 340 HIS 0.016 0.004 HIS D 101 PHE 0.067 0.013 PHE B 262 TYR 0.172 0.023 TYR C 279 ARG 0.011 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.17211 ( 785) hydrogen bonds : angle 8.27068 ( 2112) covalent geometry : bond 0.01258 (16165) covalent geometry : angle 1.83294 (21877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7701 (mtp) cc_final: 0.6814 (mtm) REVERT: B 51 ASP cc_start: 0.8291 (m-30) cc_final: 0.8052 (t0) REVERT: B 60 SER cc_start: 0.8750 (t) cc_final: 0.8499 (p) REVERT: B 82 MET cc_start: 0.8573 (tpt) cc_final: 0.8328 (tpp) REVERT: B 190 MET cc_start: 0.8022 (mtm) cc_final: 0.7630 (mtp) REVERT: B 240 TYR cc_start: 0.7742 (t80) cc_final: 0.7531 (t80) REVERT: B 241 GLU cc_start: 0.7883 (tt0) cc_final: 0.7515 (mp0) REVERT: B 269 MET cc_start: 0.8780 (mtm) cc_final: 0.8526 (mtm) REVERT: B 299 MET cc_start: 0.8486 (mtp) cc_final: 0.8234 (mtp) REVERT: B 313 MET cc_start: 0.8645 (tpp) cc_final: 0.8332 (tpt) REVERT: B 334 GLU cc_start: 0.7589 (pm20) cc_final: 0.7091 (pm20) REVERT: B 355 MET cc_start: 0.8818 (tpp) cc_final: 0.8576 (mmm) REVERT: C 44 MET cc_start: 0.6554 (mtp) cc_final: 0.5859 (mtp) REVERT: C 47 MET cc_start: 0.7207 (tpp) cc_final: 0.6960 (ptt) REVERT: C 91 TYR cc_start: 0.8174 (t80) cc_final: 0.7779 (m-80) REVERT: C 162 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.7956 (t0) REVERT: C 176 MET cc_start: 0.8132 (mmm) cc_final: 0.7889 (mmt) REVERT: C 221 LEU cc_start: 0.8704 (tp) cc_final: 0.8324 (pp) REVERT: C 291 LYS cc_start: 0.7820 (tttt) cc_final: 0.6854 (mttt) REVERT: C 326 LYS cc_start: 0.8952 (tppp) cc_final: 0.8212 (pmtt) REVERT: D 51 ASP cc_start: 0.8482 (m-30) cc_final: 0.8097 (p0) REVERT: D 162 ASN cc_start: 0.8207 (t0) cc_final: 0.7010 (t0) REVERT: D 227 MET cc_start: 0.7494 (tpt) cc_final: 0.6882 (tpt) REVERT: D 313 MET cc_start: 0.7997 (tpp) cc_final: 0.7791 (tpp) REVERT: D 317 ILE cc_start: 0.8443 (tp) cc_final: 0.8238 (pt) REVERT: P 36 PHE cc_start: 0.8618 (t80) cc_final: 0.8293 (t80) REVERT: P 64 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (pp30) REVERT: P 65 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.7572 (m90) REVERT: P 66 MET cc_start: 0.8549 (mtt) cc_final: 0.7826 (mtm) REVERT: P 364 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7874 (mtt-85) REVERT: P 394 GLN cc_start: 0.8853 (mp10) cc_final: 0.8586 (pm20) REVERT: P 412 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: P 539 MET cc_start: 0.8498 (tpp) cc_final: 0.8194 (mmm) REVERT: P 547 MET cc_start: 0.8314 (mmm) cc_final: 0.8001 (mmm) outliers start: 32 outliers final: 9 residues processed: 264 average time/residue: 1.5050 time to fit residues: 435.5407 Evaluate side-chains 148 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 64 GLN Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain R residue 45 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 79 optimal weight: 0.4980 chunk 154 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 49 GLN C 246 GLN D 59 GLN P 320 HIS P 395 HIS P 441 ASN P 487 HIS R 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.122254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095604 restraints weight = 37565.489| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.50 r_work: 0.3658 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16165 Z= 0.146 Angle : 0.702 12.047 21877 Z= 0.354 Chirality : 0.044 0.198 2406 Planarity : 0.004 0.058 2821 Dihedral : 9.614 171.934 2243 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.35 % Allowed : 10.65 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.19), residues: 1971 helix: -0.37 (0.16), residues: 915 sheet: -0.52 (0.30), residues: 249 loop : 0.54 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 340 HIS 0.008 0.001 HIS R 108 PHE 0.025 0.002 PHE P 414 TYR 0.020 0.002 TYR P 633 ARG 0.008 0.001 ARG C 95 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 785) hydrogen bonds : angle 5.54025 ( 2112) covalent geometry : bond 0.00319 (16165) covalent geometry : angle 0.70250 (21877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.785 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: B 51 ASP cc_start: 0.8308 (m-30) cc_final: 0.8061 (t0) REVERT: B 72 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5246 (pt0) REVERT: B 123 MET cc_start: 0.8869 (mmp) cc_final: 0.8626 (mmm) REVERT: B 190 MET cc_start: 0.8632 (mtm) cc_final: 0.8376 (mtp) REVERT: B 205 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7983 (mp0) REVERT: B 326 LYS cc_start: 0.7614 (pmtt) cc_final: 0.7130 (tmmt) REVERT: C 291 LYS cc_start: 0.8632 (tttt) cc_final: 0.8071 (mttt) REVERT: C 370 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8151 (m) REVERT: D 123 MET cc_start: 0.8262 (tpp) cc_final: 0.8033 (tpp) REVERT: D 227 MET cc_start: 0.8172 (tpt) cc_final: 0.7836 (tpt) REVERT: P 1 MET cc_start: 0.8670 (pmt) cc_final: 0.8454 (pmm) REVERT: P 65 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7461 (m90) REVERT: P 112 THR cc_start: 0.8009 (m) cc_final: 0.7764 (p) REVERT: P 412 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: P 539 MET cc_start: 0.8097 (tpp) cc_final: 0.7498 (mmm) REVERT: P 675 MET cc_start: 0.7976 (mmm) cc_final: 0.7709 (tpt) REVERT: P 715 TRP cc_start: 0.9111 (m100) cc_final: 0.8796 (m100) REVERT: R 77 MET cc_start: 0.8222 (mmp) cc_final: 0.7674 (mmm) REVERT: R 138 ASN cc_start: 0.8770 (p0) cc_final: 0.8467 (p0) outliers start: 40 outliers final: 16 residues processed: 203 average time/residue: 1.3444 time to fit residues: 302.4672 Evaluate side-chains 147 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain P residue 30 GLU Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 412 GLN Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 38 ARG Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 108 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 150 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 371 HIS C 12 ASN D 59 GLN R 108 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.119526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.092345 restraints weight = 37879.870| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.52 r_work: 0.3583 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16165 Z= 0.239 Angle : 0.727 12.887 21877 Z= 0.359 Chirality : 0.046 0.207 2406 Planarity : 0.005 0.043 2821 Dihedral : 8.987 178.884 2229 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.88 % Allowed : 12.59 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.15 (0.19), residues: 1971 helix: -0.17 (0.17), residues: 928 sheet: -0.46 (0.34), residues: 215 loop : 0.38 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP P 651 HIS 0.015 0.001 HIS R 108 PHE 0.024 0.002 PHE R 13 TYR 0.017 0.002 TYR C 91 ARG 0.006 0.001 ARG P 601 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 785) hydrogen bonds : angle 5.45242 ( 2112) covalent geometry : bond 0.00567 (16165) covalent geometry : angle 0.72690 (21877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 1.769 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 51 ASP cc_start: 0.8344 (m-30) cc_final: 0.7985 (t0) REVERT: B 190 MET cc_start: 0.8743 (mtm) cc_final: 0.8515 (mtp) REVERT: B 205 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8086 (mp0) REVERT: B 326 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: B 355 MET cc_start: 0.8940 (mmm) cc_final: 0.8562 (mtm) REVERT: C 72 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: C 291 LYS cc_start: 0.8708 (tttt) cc_final: 0.8071 (mptp) REVERT: C 370 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (m) REVERT: D 123 MET cc_start: 0.8368 (tpp) cc_final: 0.8057 (tpp) REVERT: D 166 TYR cc_start: 0.8108 (t80) cc_final: 0.7633 (t80) REVERT: D 227 MET cc_start: 0.8194 (tpt) cc_final: 0.7961 (tpt) REVERT: P 9 ASP cc_start: 0.8164 (p0) cc_final: 0.7948 (p0) REVERT: P 66 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7700 (ptp) REVERT: P 112 THR cc_start: 0.8147 (m) cc_final: 0.7872 (p) REVERT: P 468 GLU cc_start: 0.8228 (tp30) cc_final: 0.7785 (mp0) REVERT: P 650 MET cc_start: 0.8390 (mpt) cc_final: 0.8102 (mmp) REVERT: P 675 MET cc_start: 0.7995 (mmm) cc_final: 0.7743 (tpt) REVERT: R 1 MET cc_start: 0.3250 (ptp) cc_final: 0.2240 (pmm) REVERT: R 37 MET cc_start: 0.8172 (ptp) cc_final: 0.7807 (ptp) REVERT: R 38 ARG cc_start: 0.7713 (mpt-90) cc_final: 0.7452 (mmt90) REVERT: R 72 MET cc_start: 0.8683 (pp-130) cc_final: 0.8250 (pp-130) REVERT: R 75 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8327 (ttm170) REVERT: R 77 MET cc_start: 0.7776 (mmp) cc_final: 0.7330 (mmm) REVERT: R 138 ASN cc_start: 0.8854 (p0) cc_final: 0.8582 (p0) REVERT: R 145 MET cc_start: 0.9337 (ppp) cc_final: 0.8949 (pp-130) outliers start: 49 outliers final: 20 residues processed: 173 average time/residue: 1.2820 time to fit residues: 247.0277 Evaluate side-chains 151 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 210 GLU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.120102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.092933 restraints weight = 37820.957| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.53 r_work: 0.3599 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16165 Z= 0.177 Angle : 0.656 11.924 21877 Z= 0.321 Chirality : 0.044 0.187 2406 Planarity : 0.004 0.040 2821 Dihedral : 8.008 176.400 2221 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.94 % Allowed : 12.35 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.15 (0.19), residues: 1971 helix: 0.14 (0.17), residues: 932 sheet: -0.47 (0.32), residues: 245 loop : 0.55 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.049 0.002 PHE R 13 TYR 0.011 0.002 TYR P 69 ARG 0.005 0.000 ARG P 711 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 785) hydrogen bonds : angle 5.18194 ( 2112) covalent geometry : bond 0.00416 (16165) covalent geometry : angle 0.65647 (21877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 1.904 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 51 ASP cc_start: 0.8370 (m-30) cc_final: 0.7996 (t0) REVERT: B 190 MET cc_start: 0.8703 (mtm) cc_final: 0.8435 (mtp) REVERT: B 326 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7188 (tmmt) REVERT: B 355 MET cc_start: 0.8925 (mmm) cc_final: 0.8538 (mtm) REVERT: C 66 THR cc_start: 0.8311 (m) cc_final: 0.8043 (p) REVERT: C 72 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6290 (pt0) REVERT: C 291 LYS cc_start: 0.8680 (tttt) cc_final: 0.8032 (mptp) REVERT: C 370 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8402 (m) REVERT: D 166 TYR cc_start: 0.8180 (t80) cc_final: 0.7519 (t80) REVERT: D 227 MET cc_start: 0.8178 (tpt) cc_final: 0.7677 (tpt) REVERT: D 286 ASP cc_start: 0.6481 (t0) cc_final: 0.5918 (p0) REVERT: P 9 ASP cc_start: 0.8147 (p0) cc_final: 0.7936 (p0) REVERT: P 65 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7818 (t70) REVERT: P 66 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7705 (ptp) REVERT: P 112 THR cc_start: 0.8172 (m) cc_final: 0.7904 (p) REVERT: P 468 GLU cc_start: 0.8190 (tp30) cc_final: 0.7764 (mp0) REVERT: P 501 SER cc_start: 0.8136 (m) cc_final: 0.7589 (p) REVERT: P 598 GLN cc_start: 0.8994 (tt0) cc_final: 0.8491 (tm-30) REVERT: P 650 MET cc_start: 0.8608 (mpt) cc_final: 0.8253 (mpp) REVERT: P 675 MET cc_start: 0.7970 (mmm) cc_final: 0.7697 (tpt) REVERT: R 1 MET cc_start: 0.2529 (ptp) cc_final: 0.1552 (pmm) REVERT: R 37 MET cc_start: 0.8102 (ptp) cc_final: 0.7818 (ptp) REVERT: R 77 MET cc_start: 0.7784 (mmp) cc_final: 0.7370 (mmm) REVERT: R 145 MET cc_start: 0.9276 (ppp) cc_final: 0.8910 (pp-130) outliers start: 50 outliers final: 19 residues processed: 172 average time/residue: 1.4367 time to fit residues: 276.1315 Evaluate side-chains 153 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.092261 restraints weight = 36538.680| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.15 r_work: 0.3619 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16165 Z= 0.178 Angle : 0.647 10.424 21877 Z= 0.315 Chirality : 0.043 0.163 2406 Planarity : 0.004 0.039 2821 Dihedral : 7.666 172.186 2221 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.65 % Allowed : 13.71 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.30 (0.19), residues: 1971 helix: 0.33 (0.17), residues: 918 sheet: -0.49 (0.31), residues: 248 loop : 0.55 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.047 0.002 PHE R 13 TYR 0.015 0.001 TYR C 91 ARG 0.011 0.000 ARG R 75 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 785) hydrogen bonds : angle 5.07482 ( 2112) covalent geometry : bond 0.00417 (16165) covalent geometry : angle 0.64689 (21877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8324 (m-30) cc_final: 0.7942 (t0) REVERT: B 190 MET cc_start: 0.8699 (mtm) cc_final: 0.8437 (mtp) REVERT: B 205 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: B 326 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7605 (tmmt) REVERT: C 72 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6248 (pt0) REVERT: C 291 LYS cc_start: 0.8653 (tttt) cc_final: 0.7986 (mptp) REVERT: D 166 TYR cc_start: 0.8199 (t80) cc_final: 0.7511 (t80) REVERT: D 286 ASP cc_start: 0.6649 (t0) cc_final: 0.6226 (p0) REVERT: P 9 ASP cc_start: 0.7940 (p0) cc_final: 0.7716 (p0) REVERT: P 65 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7757 (t70) REVERT: P 66 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (ptp) REVERT: P 112 THR cc_start: 0.8231 (m) cc_final: 0.7993 (p) REVERT: P 468 GLU cc_start: 0.8141 (tp30) cc_final: 0.7765 (mp0) REVERT: P 501 SER cc_start: 0.8588 (m) cc_final: 0.8138 (p) REVERT: P 598 GLN cc_start: 0.9035 (tt0) cc_final: 0.8544 (tm-30) REVERT: P 650 MET cc_start: 0.8813 (mpt) cc_final: 0.8425 (mpp) REVERT: P 675 MET cc_start: 0.7765 (mmm) cc_final: 0.7501 (tpt) REVERT: R 1 MET cc_start: 0.2595 (ptp) cc_final: 0.1787 (pmm) REVERT: R 77 MET cc_start: 0.7866 (mmp) cc_final: 0.7540 (mmm) REVERT: R 110 MET cc_start: 0.7056 (mmt) cc_final: 0.6810 (mmm) REVERT: R 145 MET cc_start: 0.9271 (ppp) cc_final: 0.8926 (pp-130) outliers start: 45 outliers final: 27 residues processed: 172 average time/residue: 1.3665 time to fit residues: 262.4908 Evaluate side-chains 163 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 0.0870 chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS C 162 ASN D 59 GLN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.120583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.093600 restraints weight = 37762.004| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.52 r_work: 0.3614 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16165 Z= 0.155 Angle : 0.640 9.910 21877 Z= 0.308 Chirality : 0.043 0.152 2406 Planarity : 0.004 0.051 2821 Dihedral : 7.440 168.683 2220 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.18 % Allowed : 14.47 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.44 (0.19), residues: 1971 helix: 0.48 (0.17), residues: 917 sheet: -0.44 (0.31), residues: 248 loop : 0.59 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP P 651 HIS 0.003 0.001 HIS B 88 PHE 0.045 0.002 PHE R 13 TYR 0.011 0.001 TYR P 69 ARG 0.011 0.000 ARG R 107 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 785) hydrogen bonds : angle 4.93937 ( 2112) covalent geometry : bond 0.00363 (16165) covalent geometry : angle 0.63997 (21877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8344 (m-30) cc_final: 0.7945 (t0) REVERT: B 190 MET cc_start: 0.8672 (mtm) cc_final: 0.8437 (mtp) REVERT: B 205 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: B 326 LYS cc_start: 0.7820 (pmtt) cc_final: 0.7604 (tmmt) REVERT: C 72 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6272 (pt0) REVERT: C 291 LYS cc_start: 0.8637 (tttt) cc_final: 0.7919 (mptt) REVERT: C 370 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8336 (m) REVERT: D 72 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5978 (pt0) REVERT: D 166 TYR cc_start: 0.8188 (t80) cc_final: 0.7466 (t80) REVERT: P 65 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7687 (t70) REVERT: P 66 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7962 (ptp) REVERT: P 112 THR cc_start: 0.8255 (m) cc_final: 0.8010 (p) REVERT: P 468 GLU cc_start: 0.8139 (tp30) cc_final: 0.7761 (mp0) REVERT: P 501 SER cc_start: 0.8798 (m) cc_final: 0.8400 (p) REVERT: P 598 GLN cc_start: 0.8971 (tt0) cc_final: 0.8424 (tm-30) REVERT: P 650 MET cc_start: 0.8695 (mpt) cc_final: 0.8350 (mmp) REVERT: R 1 MET cc_start: 0.2655 (ptp) cc_final: 0.1637 (pmm) REVERT: R 37 MET cc_start: 0.8264 (ptp) cc_final: 0.8033 (ptp) REVERT: R 52 MET cc_start: 0.6738 (mmt) cc_final: 0.6344 (mmt) REVERT: R 72 MET cc_start: 0.8854 (ppp) cc_final: 0.8568 (ppp) REVERT: R 75 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.8212 (ttt180) REVERT: R 138 ASN cc_start: 0.8063 (p0) cc_final: 0.7659 (OUTLIER) REVERT: R 145 MET cc_start: 0.9343 (ppp) cc_final: 0.9010 (pp-130) outliers start: 54 outliers final: 27 residues processed: 170 average time/residue: 1.3306 time to fit residues: 250.8303 Evaluate side-chains 158 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 162 ASN C 371 HIS D 59 GLN ** P 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.119689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.092536 restraints weight = 37956.833| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.51 r_work: 0.3589 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16165 Z= 0.203 Angle : 0.677 10.945 21877 Z= 0.326 Chirality : 0.044 0.159 2406 Planarity : 0.004 0.039 2821 Dihedral : 7.365 158.336 2220 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.47 % Allowed : 14.88 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.36 (0.19), residues: 1971 helix: 0.42 (0.17), residues: 914 sheet: -0.40 (0.32), residues: 232 loop : 0.49 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP P 651 HIS 0.003 0.001 HIS D 161 PHE 0.043 0.002 PHE R 13 TYR 0.013 0.002 TYR C 91 ARG 0.006 0.000 ARG R 107 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 785) hydrogen bonds : angle 4.99993 ( 2112) covalent geometry : bond 0.00479 (16165) covalent geometry : angle 0.67658 (21877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8304 (m-30) cc_final: 0.7858 (t0) REVERT: B 190 MET cc_start: 0.8683 (mtm) cc_final: 0.8425 (mtp) REVERT: B 205 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: B 241 GLU cc_start: 0.7996 (tt0) cc_final: 0.7484 (mm-30) REVERT: C 72 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6494 (tt0) REVERT: C 291 LYS cc_start: 0.8637 (tttt) cc_final: 0.7948 (mptp) REVERT: C 370 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8373 (m) REVERT: D 25 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7558 (p0) REVERT: D 166 TYR cc_start: 0.8248 (t80) cc_final: 0.7493 (t80) REVERT: P 65 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7632 (t70) REVERT: P 66 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8012 (ptp) REVERT: P 112 THR cc_start: 0.8278 (m) cc_final: 0.8051 (p) REVERT: P 264 ASP cc_start: 0.8741 (p0) cc_final: 0.8414 (t70) REVERT: P 468 GLU cc_start: 0.8131 (tp30) cc_final: 0.7856 (mp0) REVERT: P 501 SER cc_start: 0.8809 (m) cc_final: 0.8458 (p) REVERT: P 598 GLN cc_start: 0.8989 (tt0) cc_final: 0.8449 (tm-30) REVERT: P 650 MET cc_start: 0.8712 (mpt) cc_final: 0.8381 (mpp) REVERT: P 675 MET cc_start: 0.7537 (mmm) cc_final: 0.7296 (tpt) REVERT: R 1 MET cc_start: 0.2809 (ptp) cc_final: 0.2029 (pmm) REVERT: R 37 MET cc_start: 0.8263 (ptp) cc_final: 0.7884 (ptp) REVERT: R 72 MET cc_start: 0.8837 (ppp) cc_final: 0.8626 (ppp) REVERT: R 77 MET cc_start: 0.7895 (mmm) cc_final: 0.7474 (mmm) REVERT: R 138 ASN cc_start: 0.8318 (p0) cc_final: 0.7988 (t0) REVERT: R 145 MET cc_start: 0.9320 (ppp) cc_final: 0.8979 (pp-130) outliers start: 42 outliers final: 27 residues processed: 162 average time/residue: 1.3547 time to fit residues: 243.6636 Evaluate side-chains 159 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 165 optimal weight: 0.3980 chunk 62 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 101 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN P 31 ASN ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.121576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.094805 restraints weight = 37568.342| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.50 r_work: 0.3636 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16165 Z= 0.124 Angle : 0.627 11.933 21877 Z= 0.300 Chirality : 0.042 0.158 2406 Planarity : 0.004 0.037 2821 Dihedral : 7.060 157.150 2220 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.29 % Allowed : 15.41 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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 (0.19), residues: 1971 helix: 0.58 (0.17), residues: 923 sheet: -0.38 (0.31), residues: 250 loop : 0.60 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 249 HIS 0.003 0.001 HIS B 88 PHE 0.045 0.001 PHE R 13 TYR 0.016 0.001 TYR P 44 ARG 0.007 0.000 ARG R 107 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 785) hydrogen bonds : angle 4.75971 ( 2112) covalent geometry : bond 0.00283 (16165) covalent geometry : angle 0.62681 (21877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8289 (m-30) cc_final: 0.7913 (t0) REVERT: B 72 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5828 (pt0) REVERT: B 190 MET cc_start: 0.8648 (mtm) cc_final: 0.8364 (mtp) REVERT: B 205 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: C 82 MET cc_start: 0.7854 (tpt) cc_final: 0.7279 (tpt) REVERT: C 291 LYS cc_start: 0.8583 (tttt) cc_final: 0.7901 (mptp) REVERT: C 370 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8290 (m) REVERT: D 72 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5654 (pt0) REVERT: D 325 MET cc_start: 0.8424 (mmp) cc_final: 0.8221 (mmt) REVERT: P 65 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7633 (t70) REVERT: P 66 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8019 (ptp) REVERT: P 72 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7765 (m) REVERT: P 112 THR cc_start: 0.8237 (m) cc_final: 0.8028 (p) REVERT: P 264 ASP cc_start: 0.8783 (p0) cc_final: 0.8394 (t70) REVERT: P 468 GLU cc_start: 0.8042 (tp30) cc_final: 0.7728 (mp0) REVERT: P 501 SER cc_start: 0.8767 (m) cc_final: 0.8475 (p) REVERT: P 598 GLN cc_start: 0.8989 (tt0) cc_final: 0.8423 (tm-30) REVERT: P 650 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8306 (mpp) REVERT: P 675 MET cc_start: 0.7655 (mmm) cc_final: 0.7398 (tpt) REVERT: R 1 MET cc_start: 0.2522 (ptp) cc_final: 0.1933 (pmm) REVERT: R 37 MET cc_start: 0.8308 (ptp) cc_final: 0.7766 (ptp) REVERT: R 73 MET cc_start: 0.5301 (mmm) cc_final: 0.4929 (mmm) REVERT: R 77 MET cc_start: 0.8070 (mmm) cc_final: 0.7572 (mmm) REVERT: R 87 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8075 (mmm160) REVERT: R 138 ASN cc_start: 0.8117 (p0) cc_final: 0.7883 (t0) REVERT: R 145 MET cc_start: 0.9301 (ppp) cc_final: 0.8944 (pp-130) outliers start: 39 outliers final: 18 residues processed: 159 average time/residue: 1.3550 time to fit residues: 241.1656 Evaluate side-chains 150 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 115 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086521 restraints weight = 37930.090| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.49 r_work: 0.3606 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16165 Z= 0.173 Angle : 0.653 12.537 21877 Z= 0.313 Chirality : 0.043 0.156 2406 Planarity : 0.004 0.036 2821 Dihedral : 7.042 148.461 2220 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.47 % Allowed : 15.76 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.48 (0.19), residues: 1971 helix: 0.50 (0.17), residues: 929 sheet: -0.27 (0.31), residues: 247 loop : 0.58 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 249 HIS 0.003 0.001 HIS D 161 PHE 0.018 0.002 PHE R 13 TYR 0.019 0.001 TYR D 166 ARG 0.007 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 785) hydrogen bonds : angle 4.84901 ( 2112) covalent geometry : bond 0.00410 (16165) covalent geometry : angle 0.65268 (21877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8270 (m-30) cc_final: 0.7892 (t0) REVERT: B 190 MET cc_start: 0.8669 (mtm) cc_final: 0.8420 (mtp) REVERT: B 205 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 241 GLU cc_start: 0.7956 (tt0) cc_final: 0.7430 (mm-30) REVERT: B 360 GLN cc_start: 0.7973 (tp40) cc_final: 0.7685 (tp-100) REVERT: C 291 LYS cc_start: 0.8605 (tttt) cc_final: 0.7804 (mmtt) REVERT: C 370 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8350 (m) REVERT: D 72 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6040 (pt0) REVERT: P 9 ASP cc_start: 0.8106 (p0) cc_final: 0.7830 (p0) REVERT: P 65 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7867 (t70) REVERT: P 66 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8112 (ptp) REVERT: P 72 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7843 (m) REVERT: P 112 THR cc_start: 0.8277 (m) cc_final: 0.8070 (p) REVERT: P 264 ASP cc_start: 0.8825 (p0) cc_final: 0.8426 (t70) REVERT: P 468 GLU cc_start: 0.8048 (tp30) cc_final: 0.7732 (mp0) REVERT: P 501 SER cc_start: 0.8889 (m) cc_final: 0.8620 (p) REVERT: P 598 GLN cc_start: 0.8999 (tt0) cc_final: 0.8425 (tm-30) REVERT: P 650 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8395 (mpp) REVERT: P 675 MET cc_start: 0.7570 (mmm) cc_final: 0.7335 (tpt) REVERT: R 1 MET cc_start: 0.2142 (ptp) cc_final: 0.1766 (pmm) REVERT: R 37 MET cc_start: 0.8355 (ptp) cc_final: 0.7584 (ptp) REVERT: R 72 MET cc_start: 0.8454 (ppp) cc_final: 0.7933 (ppp) REVERT: R 73 MET cc_start: 0.5954 (mmm) cc_final: 0.5214 (mmm) REVERT: R 77 MET cc_start: 0.8074 (mmm) cc_final: 0.7454 (mmm) REVERT: R 87 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8093 (mmm160) REVERT: R 138 ASN cc_start: 0.8127 (p0) cc_final: 0.7918 (t0) REVERT: R 145 MET cc_start: 0.9238 (ppp) cc_final: 0.8862 (pp-130) outliers start: 42 outliers final: 25 residues processed: 164 average time/residue: 1.4266 time to fit residues: 261.1655 Evaluate side-chains 157 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 62 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0370 chunk 190 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 26 optimal weight: 0.4980 chunk 187 optimal weight: 9.9990 chunk 165 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.121358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094553 restraints weight = 37879.152| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.51 r_work: 0.3633 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16165 Z= 0.131 Angle : 0.638 13.477 21877 Z= 0.303 Chirality : 0.042 0.170 2406 Planarity : 0.004 0.037 2821 Dihedral : 6.934 149.539 2220 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.18 % Allowed : 16.00 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.58 (0.19), residues: 1971 helix: 0.59 (0.17), residues: 929 sheet: -0.24 (0.31), residues: 247 loop : 0.62 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP P 648 HIS 0.002 0.001 HIS B 88 PHE 0.049 0.001 PHE R 13 TYR 0.015 0.001 TYR P 69 ARG 0.007 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 785) hydrogen bonds : angle 4.72788 ( 2112) covalent geometry : bond 0.00304 (16165) covalent geometry : angle 0.63813 (21877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5882 (pt0) REVERT: B 190 MET cc_start: 0.8650 (mtm) cc_final: 0.8402 (mtp) REVERT: B 205 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: B 241 GLU cc_start: 0.7884 (tt0) cc_final: 0.7379 (mm-30) REVERT: C 72 GLU cc_start: 0.5390 (OUTLIER) cc_final: 0.5123 (pt0) REVERT: C 82 MET cc_start: 0.7892 (tpt) cc_final: 0.7132 (tpt) REVERT: C 291 LYS cc_start: 0.8550 (tttt) cc_final: 0.7786 (mmtt) REVERT: C 370 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (m) REVERT: D 72 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5751 (pt0) REVERT: P 9 ASP cc_start: 0.8145 (p0) cc_final: 0.7901 (p0) REVERT: P 65 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7791 (t70) REVERT: P 66 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8169 (ptp) REVERT: P 72 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7831 (p) REVERT: P 264 ASP cc_start: 0.8712 (p0) cc_final: 0.8346 (t70) REVERT: P 468 GLU cc_start: 0.8025 (tp30) cc_final: 0.7732 (mp0) REVERT: P 598 GLN cc_start: 0.8944 (tt0) cc_final: 0.8407 (tm-30) REVERT: P 650 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8398 (mpp) REVERT: P 675 MET cc_start: 0.7572 (mmm) cc_final: 0.7305 (tpt) REVERT: R 1 MET cc_start: 0.2412 (ptp) cc_final: 0.2049 (pmm) REVERT: R 72 MET cc_start: 0.8482 (ppp) cc_final: 0.7986 (ppp) REVERT: R 73 MET cc_start: 0.5739 (mmm) cc_final: 0.5185 (mmm) REVERT: R 77 MET cc_start: 0.7931 (mmm) cc_final: 0.7250 (mmm) REVERT: R 87 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.8247 (mmm160) REVERT: R 110 MET cc_start: 0.7789 (mmp) cc_final: 0.7550 (mmm) REVERT: R 138 ASN cc_start: 0.8203 (p0) cc_final: 0.7959 (t0) REVERT: R 145 MET cc_start: 0.9248 (ppp) cc_final: 0.8853 (pp-130) outliers start: 37 outliers final: 23 residues processed: 156 average time/residue: 1.2597 time to fit residues: 219.7364 Evaluate side-chains 153 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 173 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain P residue 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 388 TYR Chi-restraints excluded: chain P residue 399 GLU Chi-restraints excluded: chain P residue 413 LEU Chi-restraints excluded: chain P residue 617 MET Chi-restraints excluded: chain P residue 650 MET Chi-restraints excluded: chain R residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 191 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 144 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.120213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.093379 restraints weight = 37489.124| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.48 r_work: 0.3632 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16165 Z= 0.140 Angle : 0.642 13.010 21877 Z= 0.306 Chirality : 0.042 0.172 2406 Planarity : 0.004 0.055 2821 Dihedral : 6.843 148.668 2220 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.35 % Allowed : 16.12 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % 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: 0.62 (0.19), residues: 1971 helix: 0.62 (0.17), residues: 926 sheet: -0.16 (0.32), residues: 235 loop : 0.60 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP P 249 HIS 0.002 0.001 HIS D 161 PHE 0.017 0.001 PHE R 13 TYR 0.016 0.001 TYR D 166 ARG 0.007 0.000 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 785) hydrogen bonds : angle 4.75473 ( 2112) covalent geometry : bond 0.00327 (16165) covalent geometry : angle 0.64236 (21877) =============================================================================== Job complete usr+sys time: 11193.48 seconds wall clock time: 194 minutes 33.16 seconds (11673.16 seconds total)