Starting phenix.real_space_refine on Thu Sep 18 08:50:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfw_45565/09_2025/9cfw_45565.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfw_45565/09_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_45565/09_2025/9cfw_45565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfw_45565/09_2025/9cfw_45565.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfw_45565/09_2025/9cfw_45565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfw_45565/09_2025/9cfw_45565.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.08, per 1000 atoms: 0.26 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: 1.46 Conformation dependent library (CDL) restraints added in 744.2 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.69 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: 3.28 Time building geometry restraints manager: 1.98 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: 5.760 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG D 39 TYR 0.172 0.023 TYR C 279 PHE 0.067 0.013 PHE B 262 TRP 0.236 0.029 TRP B 340 HIS 0.016 0.004 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.01258 (16165) covalent geometry : angle 1.83294 (21877) hydrogen bonds : bond 0.17211 ( 785) hydrogen bonds : angle 8.27068 ( 2112) *********************** 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 : 0.692 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: 0.7553 time to fit residues: 217.7714 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 : 0.696 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.120694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093614 restraints weight = 37730.950| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.51 r_work: 0.3624 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2493 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= 0.186 Angle : 0.722 12.493 21877 Z= 0.362 Chirality : 0.046 0.219 2406 Planarity : 0.005 0.059 2821 Dihedral : 9.678 178.335 2243 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.41 % Allowed : 10.88 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 1971 helix: -0.47 (0.16), residues: 915 sheet: -0.59 (0.31), residues: 251 loop : 0.51 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.018 0.002 TYR P 633 PHE 0.025 0.002 PHE P 414 TRP 0.032 0.004 TRP C 340 HIS 0.009 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00432 (16165) covalent geometry : angle 0.72228 (21877) hydrogen bonds : bond 0.04310 ( 785) hydrogen bonds : angle 5.63369 ( 2112) *********************** 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 206 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.652 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: 0.8308 (m-30) cc_final: 0.8037 (t0) REVERT: B 190 MET cc_start: 0.8640 (mtm) cc_final: 0.8338 (mtp) REVERT: B 205 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7907 (mp0) REVERT: B 326 LYS cc_start: 0.7703 (pmtt) cc_final: 0.7158 (tmmt) REVERT: B 334 GLU cc_start: 0.7935 (pm20) cc_final: 0.7660 (pp20) REVERT: C 47 MET cc_start: 0.7305 (tpp) cc_final: 0.6624 (tmm) REVERT: C 227 MET cc_start: 0.8645 (tpp) cc_final: 0.8419 (mmt) REVERT: C 291 LYS cc_start: 0.8679 (tttt) cc_final: 0.8029 (mptp) REVERT: C 370 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8271 (m) REVERT: D 123 MET cc_start: 0.8349 (tpp) cc_final: 0.8143 (tpp) REVERT: D 166 TYR cc_start: 0.8311 (t80) cc_final: 0.7473 (t80) REVERT: D 227 MET cc_start: 0.8219 (tpt) cc_final: 0.7887 (tpt) REVERT: P 1 MET cc_start: 0.8849 (pmt) cc_final: 0.8547 (pmm) REVERT: P 112 THR cc_start: 0.8067 (m) cc_final: 0.7817 (p) REVERT: P 412 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: P 539 MET cc_start: 0.8134 (tpp) cc_final: 0.7501 (mmm) REVERT: R 1 MET cc_start: 0.1509 (mtt) cc_final: -0.0218 (pmm) REVERT: R 77 MET cc_start: 0.8254 (mmp) cc_final: 0.7418 (mmm) REVERT: R 87 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7508 (mmm160) REVERT: R 138 ASN cc_start: 0.8766 (p0) cc_final: 0.8424 (p0) outliers start: 41 outliers final: 17 residues processed: 198 average time/residue: 0.6630 time to fit residues: 145.1199 Evaluate side-chains 153 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 D residue 43 VAL Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 36 PHE 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 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 83 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 HIS D 59 GLN R 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.120286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.093158 restraints weight = 38169.793| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.56 r_work: 0.3607 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16165 Z= 0.181 Angle : 0.681 12.641 21877 Z= 0.336 Chirality : 0.044 0.180 2406 Planarity : 0.004 0.041 2821 Dihedral : 8.606 179.520 2225 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.71 % Allowed : 12.24 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.19), residues: 1971 helix: -0.09 (0.17), residues: 937 sheet: -0.43 (0.32), residues: 239 loop : 0.49 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 601 TYR 0.018 0.002 TYR C 91 PHE 0.018 0.002 PHE P 173 TRP 0.033 0.003 TRP P 648 HIS 0.017 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00424 (16165) covalent geometry : angle 0.68097 (21877) hydrogen bonds : bond 0.03937 ( 785) hydrogen bonds : angle 5.30913 ( 2112) *********************** 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 192 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.712 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: 0.8406 (m-30) cc_final: 0.8048 (t0) REVERT: B 190 MET cc_start: 0.8703 (mtm) cc_final: 0.8454 (mtp) REVERT: B 205 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7914 (mp0) REVERT: B 326 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7130 (tmmt) REVERT: B 334 GLU cc_start: 0.7958 (pm20) cc_final: 0.7644 (pp20) REVERT: B 355 MET cc_start: 0.8930 (mmm) cc_final: 0.8376 (mtm) REVERT: C 47 MET cc_start: 0.7374 (tpp) cc_final: 0.6593 (tmm) REVERT: C 72 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6312 (pt0) REVERT: C 291 LYS cc_start: 0.8677 (tttt) cc_final: 0.8021 (mptp) REVERT: C 370 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8376 (m) REVERT: D 123 MET cc_start: 0.8258 (tpp) cc_final: 0.8012 (tpp) REVERT: D 227 MET cc_start: 0.8205 (tpt) cc_final: 0.7969 (tpt) REVERT: D 286 ASP cc_start: 0.6550 (t0) cc_final: 0.6336 (t0) REVERT: P 65 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7888 (t70) REVERT: P 66 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7512 (mtm) REVERT: P 112 THR cc_start: 0.8143 (m) cc_final: 0.7883 (p) REVERT: P 468 GLU cc_start: 0.8230 (tp30) cc_final: 0.7794 (mp0) REVERT: P 650 MET cc_start: 0.8373 (mpt) cc_final: 0.8085 (mmp) REVERT: P 675 MET cc_start: 0.7797 (mmm) cc_final: 0.7542 (tpt) REVERT: R 1 MET cc_start: 0.1471 (mtt) cc_final: 0.0815 (ptp) REVERT: R 37 MET cc_start: 0.8189 (ptp) cc_final: 0.7834 (ptp) REVERT: R 112 ASN cc_start: 0.9413 (m-40) cc_final: 0.9127 (m110) REVERT: R 138 ASN cc_start: 0.8665 (p0) cc_final: 0.8316 (p0) outliers start: 46 outliers final: 22 residues processed: 180 average time/residue: 0.6524 time to fit residues: 130.0792 Evaluate side-chains 154 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 72 GLU 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 370 VAL Chi-restraints excluded: chain P residue 31 ASN Chi-restraints excluded: chain P residue 65 HIS Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain P residue 101 VAL 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 100 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.119680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.092496 restraints weight = 37795.397| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.53 r_work: 0.3595 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16165 Z= 0.190 Angle : 0.663 11.262 21877 Z= 0.324 Chirality : 0.044 0.205 2406 Planarity : 0.004 0.040 2821 Dihedral : 7.915 173.213 2222 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.88 % Allowed : 13.24 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.19), residues: 1971 helix: 0.15 (0.17), residues: 934 sheet: -0.50 (0.34), residues: 217 loop : 0.54 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 37 TYR 0.015 0.002 TYR D 166 PHE 0.026 0.002 PHE R 13 TRP 0.026 0.003 TRP C 340 HIS 0.004 0.001 HIS R 108 Details of bonding type rmsd covalent geometry : bond 0.00448 (16165) covalent geometry : angle 0.66274 (21877) hydrogen bonds : bond 0.03673 ( 785) hydrogen bonds : angle 5.14954 ( 2112) *********************** 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 189 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 140 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8366 (m-30) cc_final: 0.7983 (t0) REVERT: B 190 MET cc_start: 0.8703 (mtm) cc_final: 0.8458 (mtp) REVERT: B 326 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7432 (tmmt) REVERT: B 334 GLU cc_start: 0.8019 (pm20) cc_final: 0.7674 (pp20) REVERT: C 66 THR cc_start: 0.8297 (m) cc_final: 0.8019 (p) REVERT: C 72 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6209 (pt0) REVERT: C 291 LYS cc_start: 0.8670 (tttt) cc_final: 0.8031 (mptp) REVERT: C 370 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8438 (m) REVERT: D 286 ASP cc_start: 0.6745 (t0) cc_final: 0.6205 (p0) REVERT: P 9 ASP cc_start: 0.8177 (p0) cc_final: 0.7927 (p0) REVERT: P 65 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7689 (t70) REVERT: P 66 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (ptp) REVERT: P 112 THR cc_start: 0.8191 (m) cc_final: 0.7925 (p) REVERT: P 468 GLU cc_start: 0.8151 (tp30) cc_final: 0.7755 (mp0) REVERT: P 598 GLN cc_start: 0.9046 (tt0) cc_final: 0.8558 (tm-30) REVERT: P 650 MET cc_start: 0.8629 (mpt) cc_final: 0.8223 (mpp) REVERT: R 77 MET cc_start: 0.8366 (mmm) cc_final: 0.8072 (mmm) REVERT: R 87 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.7987 (mmm160) REVERT: R 101 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8960 (pt) REVERT: R 138 ASN cc_start: 0.8618 (p0) cc_final: 0.8209 (p0) REVERT: R 145 MET cc_start: 0.9236 (ppp) cc_final: 0.8857 (pp-130) outliers start: 49 outliers final: 21 residues processed: 175 average time/residue: 0.6054 time to fit residues: 118.1048 Evaluate side-chains 159 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 72 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 227 MET 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 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 87 ARG Chi-restraints excluded: chain R residue 101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 0.1980 chunk 130 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.120625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.093646 restraints weight = 37894.082| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.53 r_work: 0.3618 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3534 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= 0.150 Angle : 0.637 10.723 21877 Z= 0.310 Chirality : 0.043 0.156 2406 Planarity : 0.004 0.038 2821 Dihedral : 7.625 172.861 2222 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.29 % Allowed : 13.65 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1971 helix: 0.33 (0.17), residues: 923 sheet: -0.45 (0.32), residues: 242 loop : 0.66 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 711 TYR 0.021 0.001 TYR D 166 PHE 0.053 0.002 PHE R 13 TRP 0.033 0.003 TRP P 651 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00351 (16165) covalent geometry : angle 0.63709 (21877) hydrogen bonds : bond 0.03470 ( 785) hydrogen bonds : angle 4.99833 ( 2112) *********************** 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 192 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8339 (m-30) cc_final: 0.7971 (t0) REVERT: B 190 MET cc_start: 0.8676 (mtm) cc_final: 0.8419 (mtp) REVERT: B 326 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7383 (tmmt) REVERT: B 334 GLU cc_start: 0.8018 (pm20) cc_final: 0.7663 (pp20) REVERT: C 44 MET cc_start: 0.7531 (mtp) cc_final: 0.6363 (mtm) REVERT: C 72 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.6108 (pt0) REVERT: C 291 LYS cc_start: 0.8640 (tttt) cc_final: 0.7957 (mptp) REVERT: D 286 ASP cc_start: 0.6598 (t0) cc_final: 0.6193 (p0) REVERT: P 9 ASP cc_start: 0.7978 (p0) cc_final: 0.7776 (p0) REVERT: P 11 VAL cc_start: 0.6780 (t) cc_final: 0.6380 (m) REVERT: P 65 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7586 (t70) REVERT: P 66 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.8034 (ptp) REVERT: P 112 THR cc_start: 0.8208 (m) cc_final: 0.7968 (p) REVERT: P 382 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.5882 (tm) REVERT: P 468 GLU cc_start: 0.8084 (tp30) cc_final: 0.7726 (mp0) REVERT: P 501 SER cc_start: 0.8523 (m) cc_final: 0.8051 (p) REVERT: P 598 GLN cc_start: 0.8998 (tt0) cc_final: 0.8522 (tm-30) REVERT: P 650 MET cc_start: 0.8653 (mpt) cc_final: 0.8272 (mpp) REVERT: P 675 MET cc_start: 0.8022 (mmm) cc_final: 0.7770 (tpt) REVERT: R 1 MET cc_start: 0.2384 (ptp) cc_final: 0.1665 (pmm) REVERT: R 77 MET cc_start: 0.8491 (mmm) cc_final: 0.8064 (mmm) REVERT: R 87 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8027 (mmm160) REVERT: R 101 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8904 (pt) REVERT: R 138 ASN cc_start: 0.8686 (p0) cc_final: 0.8243 (p0) REVERT: R 145 MET cc_start: 0.9193 (ppp) cc_final: 0.8840 (pp-130) outliers start: 56 outliers final: 26 residues processed: 173 average time/residue: 0.6144 time to fit residues: 118.4634 Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 122 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 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 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 31 ASN 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 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 382 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 75 ARG Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 101 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 179 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0870 chunk 113 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS C 162 ASN D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.120971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.094073 restraints weight = 37648.654| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.50 r_work: 0.3617 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3719 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= 0.157 Angle : 0.641 10.829 21877 Z= 0.308 Chirality : 0.043 0.149 2406 Planarity : 0.004 0.037 2821 Dihedral : 7.422 168.703 2221 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.35 % Allowed : 14.47 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1971 helix: 0.47 (0.17), residues: 920 sheet: -0.48 (0.31), residues: 248 loop : 0.67 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 711 TYR 0.023 0.001 TYR D 166 PHE 0.045 0.002 PHE R 13 TRP 0.037 0.003 TRP P 648 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00368 (16165) covalent geometry : angle 0.64109 (21877) hydrogen bonds : bond 0.03400 ( 785) hydrogen bonds : angle 4.91196 ( 2112) *********************** 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 195 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 138 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8334 (m-30) cc_final: 0.7940 (t0) REVERT: B 190 MET cc_start: 0.8671 (mtm) cc_final: 0.8409 (mtp) REVERT: B 202 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (t) REVERT: B 326 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7581 (tmmt) REVERT: B 334 GLU cc_start: 0.7976 (pm20) cc_final: 0.7635 (pp20) REVERT: C 72 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6140 (pt0) REVERT: C 291 LYS cc_start: 0.8606 (tttt) cc_final: 0.7852 (mmtt) REVERT: C 370 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8342 (m) REVERT: D 25 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7530 (OUTLIER) REVERT: D 286 ASP cc_start: 0.6559 (t0) cc_final: 0.6269 (p0) REVERT: P 11 VAL cc_start: 0.6723 (t) cc_final: 0.6435 (m) REVERT: P 65 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7562 (t-170) REVERT: P 66 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (ptp) REVERT: P 112 THR cc_start: 0.8253 (m) cc_final: 0.8016 (p) REVERT: P 382 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.5881 (tm) REVERT: P 468 GLU cc_start: 0.8109 (tp30) cc_final: 0.7741 (mp0) REVERT: P 501 SER cc_start: 0.8792 (m) cc_final: 0.8386 (p) REVERT: P 598 GLN cc_start: 0.8957 (tt0) cc_final: 0.8404 (tm-30) REVERT: P 650 MET cc_start: 0.8608 (mpt) cc_final: 0.8260 (mpp) REVERT: R 1 MET cc_start: 0.2271 (ptp) cc_final: 0.1877 (pmm) REVERT: R 37 MET cc_start: 0.8412 (ptp) cc_final: 0.8160 (ptp) REVERT: R 77 MET cc_start: 0.8579 (mmm) cc_final: 0.8068 (mmm) REVERT: R 86 ILE cc_start: 0.9386 (pp) cc_final: 0.9177 (pp) REVERT: R 87 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8017 (mmm160) REVERT: R 138 ASN cc_start: 0.8631 (p0) cc_final: 0.8158 (p0) REVERT: R 145 MET cc_start: 0.9124 (ppp) cc_final: 0.8842 (pp-130) outliers start: 57 outliers final: 28 residues processed: 178 average time/residue: 0.6033 time to fit residues: 119.8465 Evaluate side-chains 168 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 122 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 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 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 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 31 ASN 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 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 382 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 106 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 165 optimal weight: 0.0970 chunk 146 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN B 92 ASN C 162 ASN D 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.121774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.094965 restraints weight = 37550.522| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.51 r_work: 0.3633 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3888 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= 0.135 Angle : 0.632 11.445 21877 Z= 0.303 Chirality : 0.042 0.148 2406 Planarity : 0.004 0.037 2821 Dihedral : 7.227 164.605 2221 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.65 % Allowed : 15.29 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1971 helix: 0.55 (0.17), residues: 927 sheet: -0.33 (0.32), residues: 242 loop : 0.70 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 711 TYR 0.015 0.001 TYR D 166 PHE 0.046 0.002 PHE R 13 TRP 0.023 0.002 TRP P 648 HIS 0.003 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00313 (16165) covalent geometry : angle 0.63232 (21877) hydrogen bonds : bond 0.03273 ( 785) hydrogen bonds : angle 4.79354 ( 2112) *********************** 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 178 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8370 (m-30) cc_final: 0.8004 (t0) REVERT: B 72 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5731 (pt0) REVERT: B 190 MET cc_start: 0.8651 (mtm) cc_final: 0.8399 (mtp) REVERT: B 202 THR cc_start: 0.9257 (p) cc_final: 0.9049 (t) REVERT: C 47 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4229 (pmm) REVERT: C 72 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.6111 (pt0) REVERT: C 291 LYS cc_start: 0.8591 (tttt) cc_final: 0.7921 (mptp) REVERT: C 370 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (m) REVERT: D 25 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7532 (OUTLIER) REVERT: D 72 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5714 (pt0) REVERT: P 11 VAL cc_start: 0.6597 (t) cc_final: 0.6382 (m) REVERT: P 65 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7508 (t-170) REVERT: P 66 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8103 (ptp) REVERT: P 112 THR cc_start: 0.8205 (m) cc_final: 0.7996 (p) REVERT: P 264 ASP cc_start: 0.8802 (p0) cc_final: 0.8440 (t70) REVERT: P 382 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5990 (tm) REVERT: P 468 GLU cc_start: 0.8076 (tp30) cc_final: 0.7737 (mp0) REVERT: P 501 SER cc_start: 0.8769 (m) cc_final: 0.8390 (p) REVERT: P 598 GLN cc_start: 0.8960 (tt0) cc_final: 0.8402 (tm-30) REVERT: P 650 MET cc_start: 0.8656 (mpt) cc_final: 0.8277 (mpp) REVERT: P 675 MET cc_start: 0.7760 (mmm) cc_final: 0.7473 (tpt) REVERT: R 77 MET cc_start: 0.8650 (mmm) cc_final: 0.8138 (mmm) REVERT: R 87 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.7968 (mmm160) REVERT: R 138 ASN cc_start: 0.8621 (p0) cc_final: 0.8225 (p0) REVERT: R 145 MET cc_start: 0.9183 (ppp) cc_final: 0.8824 (pp-130) outliers start: 45 outliers final: 21 residues processed: 166 average time/residue: 0.6138 time to fit residues: 113.6792 Evaluate side-chains 156 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 232 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 GLU 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 44 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR 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 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 382 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 28 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 183 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN C 371 HIS D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.119837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.092697 restraints weight = 37896.259| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.50 r_work: 0.3581 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16165 Z= 0.225 Angle : 0.710 12.493 21877 Z= 0.342 Chirality : 0.045 0.175 2406 Planarity : 0.004 0.039 2821 Dihedral : 7.267 151.396 2221 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.88 % Allowed : 15.24 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.19), residues: 1971 helix: 0.42 (0.17), residues: 923 sheet: -0.39 (0.33), residues: 219 loop : 0.59 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.020 0.002 TYR D 166 PHE 0.047 0.002 PHE R 13 TRP 0.025 0.003 TRP P 249 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00531 (16165) covalent geometry : angle 0.71028 (21877) hydrogen bonds : bond 0.03605 ( 785) hydrogen bonds : angle 5.01476 ( 2112) *********************** 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 180 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.3960 (pmm) REVERT: B 51 ASP cc_start: 0.8360 (m-30) cc_final: 0.7907 (t0) REVERT: B 190 MET cc_start: 0.8687 (mtm) cc_final: 0.8441 (mtp) REVERT: B 241 GLU cc_start: 0.7965 (tt0) cc_final: 0.7435 (mm-30) REVERT: C 47 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.4637 (pmm) REVERT: C 72 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6506 (pt0) REVERT: C 82 MET cc_start: 0.8113 (tpt) cc_final: 0.7512 (tpt) REVERT: C 123 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7658 (tpt) REVERT: C 291 LYS cc_start: 0.8626 (tttt) cc_final: 0.7939 (mptp) REVERT: C 370 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8375 (m) REVERT: D 25 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7578 (p0) REVERT: D 325 MET cc_start: 0.8468 (mmp) cc_final: 0.8229 (mmt) REVERT: P 65 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7773 (t-170) REVERT: P 66 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8159 (ptp) REVERT: P 72 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (m) REVERT: P 112 THR cc_start: 0.8273 (m) cc_final: 0.8064 (p) REVERT: P 264 ASP cc_start: 0.8746 (p0) cc_final: 0.8398 (t70) REVERT: P 382 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6118 (tm) REVERT: P 468 GLU cc_start: 0.8077 (tp30) cc_final: 0.7819 (mp0) REVERT: P 501 SER cc_start: 0.8861 (m) cc_final: 0.8575 (p) REVERT: P 598 GLN cc_start: 0.8970 (tt0) cc_final: 0.8431 (tm-30) REVERT: P 650 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8350 (mpp) REVERT: P 675 MET cc_start: 0.7829 (mmm) cc_final: 0.7589 (tpt) REVERT: R 1 MET cc_start: 0.3347 (pmm) cc_final: 0.3069 (pmm) REVERT: R 87 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8154 (mmm160) REVERT: R 145 MET cc_start: 0.9183 (ppp) cc_final: 0.8823 (pp-130) outliers start: 49 outliers final: 30 residues processed: 168 average time/residue: 0.6037 time to fit residues: 113.1722 Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 47 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 192 ILE 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 47 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 190 MET 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 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 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 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 382 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 Chi-restraints excluded: chain R residue 136 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 100 optimal weight: 0.5980 chunk 181 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 105 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.121552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.092974 restraints weight = 35985.535| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 3.09 r_work: 0.3612 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16165 Z= 0.148 Angle : 0.669 13.168 21877 Z= 0.321 Chirality : 0.043 0.195 2406 Planarity : 0.004 0.038 2821 Dihedral : 7.082 150.695 2221 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.53 % Allowed : 16.06 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.19), residues: 1971 helix: 0.47 (0.17), residues: 926 sheet: -0.36 (0.31), residues: 247 loop : 0.66 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 10 TYR 0.015 0.001 TYR D 166 PHE 0.022 0.001 PHE R 93 TRP 0.033 0.003 TRP P 249 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00345 (16165) covalent geometry : angle 0.66916 (21877) hydrogen bonds : bond 0.03369 ( 785) hydrogen bonds : angle 4.84851 ( 2112) *********************** 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: 43 poor density : 129 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 ASP cc_start: 0.8265 (m-30) cc_final: 0.7894 (t0) REVERT: B 72 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5823 (pt0) REVERT: B 190 MET cc_start: 0.8658 (mtm) cc_final: 0.8405 (mtp) REVERT: B 241 GLU cc_start: 0.7900 (tt0) cc_final: 0.7394 (mm-30) REVERT: C 72 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6447 (pt0) REVERT: C 82 MET cc_start: 0.8012 (tpt) cc_final: 0.7444 (tpt) REVERT: C 291 LYS cc_start: 0.8580 (tttt) cc_final: 0.7793 (mmtt) REVERT: C 370 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (m) REVERT: D 25 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7545 (OUTLIER) REVERT: D 72 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6015 (pt0) REVERT: P 9 ASP cc_start: 0.8257 (p0) cc_final: 0.7913 (p0) REVERT: P 65 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7850 (t70) REVERT: P 66 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8153 (ptp) REVERT: P 72 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7866 (m) REVERT: P 264 ASP cc_start: 0.8802 (p0) cc_final: 0.8419 (t70) REVERT: P 382 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6050 (tm) REVERT: P 468 GLU cc_start: 0.8041 (tp30) cc_final: 0.7732 (mp0) REVERT: P 501 SER cc_start: 0.8886 (m) cc_final: 0.8634 (p) REVERT: P 598 GLN cc_start: 0.8996 (tt0) cc_final: 0.8415 (tm-30) REVERT: P 650 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: P 675 MET cc_start: 0.7916 (mmm) cc_final: 0.7686 (tpt) REVERT: R 1 MET cc_start: 0.3409 (pmm) cc_final: 0.3145 (pmm) REVERT: R 73 MET cc_start: 0.5677 (mmm) cc_final: 0.5062 (mmm) REVERT: R 77 MET cc_start: 0.8021 (mmm) cc_final: 0.7654 (mmm) REVERT: R 87 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8192 (mmm160) REVERT: R 138 ASN cc_start: 0.8846 (p0) cc_final: 0.8533 (t0) REVERT: R 145 MET cc_start: 0.9094 (ppp) cc_final: 0.8708 (pp-130) outliers start: 43 outliers final: 26 residues processed: 159 average time/residue: 0.6326 time to fit residues: 111.9193 Evaluate side-chains 158 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 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 190 MET 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 44 MET Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 106 THR 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 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 382 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 Chi-restraints excluded: chain R residue 136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 101 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 180 optimal weight: 7.9990 chunk 39 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 162 ASN D 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.121819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093310 restraints weight = 36147.705| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.09 r_work: 0.3617 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4161 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= 0.151 Angle : 0.679 10.986 21877 Z= 0.325 Chirality : 0.043 0.211 2406 Planarity : 0.004 0.051 2821 Dihedral : 7.043 150.082 2221 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.41 % Allowed : 16.29 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.19), residues: 1971 helix: 0.50 (0.17), residues: 925 sheet: -0.31 (0.31), residues: 247 loop : 0.64 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 10 TYR 0.014 0.001 TYR D 166 PHE 0.047 0.002 PHE R 13 TRP 0.041 0.003 TRP P 648 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00351 (16165) covalent geometry : angle 0.67906 (21877) hydrogen bonds : bond 0.03358 ( 785) hydrogen bonds : angle 4.83478 ( 2112) ********************** 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 170 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5802 (pt0) REVERT: B 132 MET cc_start: 0.8736 (ppp) cc_final: 0.8528 (ppp) REVERT: B 190 MET cc_start: 0.8666 (mtm) cc_final: 0.8406 (mtp) REVERT: B 241 GLU cc_start: 0.7900 (tt0) cc_final: 0.7381 (mm-30) REVERT: C 72 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6478 (pt0) REVERT: C 291 LYS cc_start: 0.8573 (tttt) cc_final: 0.7790 (mmtt) REVERT: C 370 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8261 (m) REVERT: D 25 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7521 (OUTLIER) REVERT: D 72 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6081 (pt0) REVERT: P 9 ASP cc_start: 0.8296 (p0) cc_final: 0.7901 (p0) REVERT: P 65 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7875 (t70) REVERT: P 66 MET cc_start: 0.8488 (mtp) cc_final: 0.8170 (ptp) REVERT: P 72 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7917 (m) REVERT: P 264 ASP cc_start: 0.8778 (p0) cc_final: 0.8403 (t70) REVERT: P 382 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6023 (tm) REVERT: P 468 GLU cc_start: 0.8024 (tp30) cc_final: 0.7724 (mp0) REVERT: P 598 GLN cc_start: 0.8991 (tt0) cc_final: 0.8407 (tm-30) REVERT: P 650 MET cc_start: 0.8530 (mpt) cc_final: 0.8237 (mpp) REVERT: P 675 MET cc_start: 0.7868 (mmm) cc_final: 0.7593 (tpt) REVERT: R 1 MET cc_start: 0.3860 (pmm) cc_final: 0.3589 (pmm) REVERT: R 77 MET cc_start: 0.8108 (mmm) cc_final: 0.7160 (mmm) REVERT: R 87 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.8268 (mmm160) REVERT: R 138 ASN cc_start: 0.8605 (p0) cc_final: 0.8334 (t0) REVERT: R 145 MET cc_start: 0.9111 (ppp) cc_final: 0.8720 (pp-130) outliers start: 41 outliers final: 25 residues processed: 162 average time/residue: 0.6659 time to fit residues: 119.7257 Evaluate side-chains 155 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain B residue 107 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 43 THR Chi-restraints excluded: chain P residue 65 HIS 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 243 ILE Chi-restraints excluded: chain P residue 336 LEU Chi-restraints excluded: chain P residue 382 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 Chi-restraints excluded: chain R residue 136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 159 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 83 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 191 optimal weight: 0.1980 chunk 58 optimal weight: 0.2980 chunk 174 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.119869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092366 restraints weight = 37655.603| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.60 r_work: 0.3572 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16165 Z= 0.134 Angle : 0.674 14.556 21877 Z= 0.322 Chirality : 0.043 0.189 2406 Planarity : 0.004 0.037 2821 Dihedral : 6.920 150.077 2221 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.06 % Allowed : 17.12 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.19), residues: 1971 helix: 0.53 (0.17), residues: 929 sheet: -0.25 (0.32), residues: 241 loop : 0.63 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 37 TYR 0.067 0.001 TYR R 100 PHE 0.040 0.002 PHE R 93 TRP 0.040 0.003 TRP P 249 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00310 (16165) covalent geometry : angle 0.67440 (21877) hydrogen bonds : bond 0.03315 ( 785) hydrogen bonds : angle 4.76643 ( 2112) =============================================================================== Job complete usr+sys time: 5517.87 seconds wall clock time: 95 minutes 7.67 seconds (5707.67 seconds total)