Starting phenix.real_space_refine on Thu Sep 26 12:21:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yy0_11001/09_2024/6yy0_11001_trim.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 101 5.16 5 C 19097 2.51 5 N 5260 2.21 5 O 5858 1.98 5 H 30826 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 265 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 61162 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 7839 Classifications: {'peptide': 508} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 489} Chain: "B" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 7393 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 7699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 7699 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1957 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "S" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 3004 Classifications: {'peptide': 188} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "b" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2274 Classifications: {'peptide': 136} Link IDs: {'TRANS': 135} Chain: "d" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 2570 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 144} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" 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: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 25.27, per 1000 atoms: 0.41 Number of scatterers: 61162 At special positions: 0 Unit cell: (149.864, 135.192, 188.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 101 16.00 P 15 15.00 Mg 5 11.99 O 5858 8.00 N 5260 7.00 C 19097 6.00 H 30826 1.00 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: 12.68 Conformation dependent library (CDL) restraints added in 4.0 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7212 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 51.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.509A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.879A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.911A pdb=" N GLY A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.997A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.623A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.738A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.638A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 removed outlier: 4.087A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.134A pdb=" N GLN A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 475 removed outlier: 4.163A pdb=" N THR A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.086A pdb=" N LEU A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 506 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.562A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.598A pdb=" N ILE B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 4.178A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.942A pdb=" N GLN B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.805A pdb=" N ALA B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 294 " --> pdb=" O ARG B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 290 through 294' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.831A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.504A pdb=" N THR B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.903A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.826A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.884A pdb=" N LEU B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 7 through 18 removed outlier: 3.573A pdb=" N ARG C 15 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.698A pdb=" N ILE C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 239 through 259 removed outlier: 3.627A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.814A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.874A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.668A pdb=" N ALA C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 296 No H-bonds generated for 'chain 'C' and resid 295 through 296' Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.772A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.707A pdb=" N GLY C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 346 removed outlier: 3.558A pdb=" N THR C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.527A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 400 " --> pdb=" O GLN C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.678A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.641A pdb=" N LYS C 455 " --> pdb=" O TYR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 476 removed outlier: 4.073A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.559A pdb=" N ALA C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.648A pdb=" N MET D 130 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 229 through 249 removed outlier: 3.671A pdb=" N ARG D 235 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 274 removed outlier: 4.089A pdb=" N THR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 288 through 298 removed outlier: 3.704A pdb=" N MET D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 removed outlier: 3.584A pdb=" N ASP D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 331 through 333 No H-bonds generated for 'chain 'D' and resid 331 through 333' Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 368 through 393 removed outlier: 3.868A pdb=" N ASP D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.505A pdb=" N LEU D 400 " --> pdb=" O MET D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 425 through 430 Processing helix chain 'D' and resid 437 through 451 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 466 through 480 removed outlier: 3.607A pdb=" N ALA D 470 " --> pdb=" O PRO D 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.642A pdb=" N THR E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 95 " --> pdb=" O PRO E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 91 through 95' Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 193 through 208 Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.564A pdb=" N ARG E 233 " --> pdb=" O PRO E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 250 removed outlier: 3.768A pdb=" N PHE E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 3.542A pdb=" N PHE E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.967A pdb=" N MET E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 320 Processing helix chain 'E' and resid 323 through 330 Processing helix chain 'E' and resid 340 through 345 Processing helix chain 'E' and resid 363 through 368 Processing helix chain 'E' and resid 368 through 396 removed outlier: 3.918A pdb=" N ASP E 390 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 400 Processing helix chain 'E' and resid 401 through 419 removed outlier: 3.672A pdb=" N LYS E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER E 419 " --> pdb=" O GLN E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 425 through 430 removed outlier: 3.726A pdb=" N GLY E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 451 removed outlier: 3.577A pdb=" N THR E 441 " --> pdb=" O PRO E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 466 through 479 removed outlier: 3.619A pdb=" N ALA E 470 " --> pdb=" O PRO E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.827A pdb=" N LEU F 95 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 180 Processing helix chain 'F' and resid 193 through 207 Processing helix chain 'F' and resid 229 through 235 removed outlier: 3.808A pdb=" N ARG F 235 " --> pdb=" O GLY F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 249 removed outlier: 3.627A pdb=" N PHE F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 276 removed outlier: 3.746A pdb=" N THR F 266 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA F 274 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 330 Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 369 through 395 removed outlier: 4.419A pdb=" N ASP F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE F 391 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 418 Processing helix chain 'F' and resid 425 through 430 Processing helix chain 'F' and resid 437 through 451 Processing helix chain 'F' and resid 457 through 461 Processing helix chain 'F' and resid 466 through 479 removed outlier: 3.617A pdb=" N ALA F 470 " --> pdb=" O PRO F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 55 Proline residue: G 40 - end of helix removed outlier: 4.516A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 100 Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.670A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.654A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 removed outlier: 3.786A pdb=" N SER G 186 " --> pdb=" O ASP G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 Processing helix chain 'G' and resid 199 through 271 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 105 through 121 removed outlier: 3.852A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.276A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 removed outlier: 3.804A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 54 removed outlier: 3.843A pdb=" N LYS J 24 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 Processing helix chain 'S' and resid 31 through 46 removed outlier: 3.542A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 56 Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'S' and resid 79 through 92 Processing helix chain 'S' and resid 93 through 96 removed outlier: 4.552A pdb=" N THR S 96 " --> pdb=" O GLY S 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 93 through 96' Processing helix chain 'S' and resid 97 through 113 removed outlier: 3.516A pdb=" N VAL S 101 " --> pdb=" O ASN S 97 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS S 112 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 142 Processing helix chain 'S' and resid 174 through 188 Processing helix chain 'b' and resid 74 through 77 Processing helix chain 'b' and resid 78 through 119 removed outlier: 3.982A pdb=" N ALA b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN b 88 " --> pdb=" O LYS b 84 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS b 89 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU b 93 " --> pdb=" O LYS b 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS b 102 " --> pdb=" O GLN b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 185 removed outlier: 3.693A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 removed outlier: 3.962A pdb=" N GLN b 209 " --> pdb=" O SER b 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 18 removed outlier: 3.628A pdb=" N ILE d 18 " --> pdb=" O PHE d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 44 removed outlier: 4.084A pdb=" N SER d 29 " --> pdb=" O ALA d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 58 Processing helix chain 'd' and resid 62 through 76 removed outlier: 3.527A pdb=" N VAL d 66 " --> pdb=" O LYS d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 87 Processing helix chain 'd' and resid 88 through 99 removed outlier: 3.944A pdb=" N GLU d 92 " --> pdb=" O GLN d 88 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 98 " --> pdb=" O LYS d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 123 Processing helix chain 'd' and resid 131 through 139 Processing helix chain 'd' and resid 140 through 143 Processing helix chain 'h' and resid 8 through 25 Processing helix chain 'h' and resid 31 through 51 removed outlier: 3.722A pdb=" N TYR h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) 1289 hydrogen bonds defined for protein. 3750 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: 20.31 Time building geometry restraints manager: 15.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 30815 1.03 - 1.22: 34 1.22 - 1.42: 12167 1.42 - 1.61: 18384 1.61 - 1.81: 191 Bond restraints: 61591 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.53e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.47e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.12e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.96e+01 ... (remaining 61586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 111736 4.78 - 9.57: 60 9.57 - 14.35: 1 14.35 - 19.14: 4 19.14 - 23.92: 2 Bond angle restraints: 111803 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 115.95 23.92 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 121.45 15.38 1.00e+00 1.00e+00 2.37e+02 ... (remaining 111798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.49: 27428 30.49 - 60.97: 1166 60.97 - 91.46: 68 91.46 - 121.94: 0 121.94 - 152.43: 1 Dihedral angle restraints: 28663 sinusoidal: 16163 harmonic: 12500 Sorted by residual: dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 147.57 152.43 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" CA GLN H 132 " pdb=" C GLN H 132 " pdb=" N ILE H 133 " pdb=" CA ILE H 133 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLN E 312 " pdb=" C GLN E 312 " pdb=" N ALA E 313 " pdb=" CA ALA E 313 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 28660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3241 0.038 - 0.076: 1165 0.076 - 0.115: 313 0.115 - 0.153: 102 0.153 - 0.191: 3 Chirality restraints: 4824 Sorted by residual: chirality pdb=" CA GLN H 132 " pdb=" N GLN H 132 " pdb=" C GLN H 132 " pdb=" CB GLN H 132 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU h 42 " pdb=" N GLU h 42 " pdb=" C GLU h 42 " pdb=" CB GLU h 42 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 4821 not shown) Planarity restraints: 9121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 457 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO C 458 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 458 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 458 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP h 5 " -0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO h 6 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO h 6 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO h 6 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 132 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.49e+00 pdb=" C GLN H 132 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN H 132 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE H 133 " 0.015 2.00e-02 2.50e+03 ... (remaining 9118 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 2139 2.14 - 2.75: 119933 2.75 - 3.37: 176628 3.37 - 3.98: 232694 3.98 - 4.60: 368630 Nonbonded interactions: 900024 Sorted by model distance: nonbonded pdb="HE21 GLN A 163 " pdb=" OE1 GLU A 165 " model vdw 1.524 2.450 nonbonded pdb=" OE1 GLU E 370 " pdb=" H GLU E 370 " model vdw 1.536 2.450 nonbonded pdb=" OG SER G 72 " pdb=" H SER G 73 " model vdw 1.557 2.450 nonbonded pdb="HH12 ARG D 45 " pdb=" O GLU D 71 " model vdw 1.558 2.450 nonbonded pdb=" O GLN B 186 " pdb="HD22 ASN B 190 " model vdw 1.558 2.450 ... (remaining 900019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) selection = chain 'B' selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 401 or (resid \ 411 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2 or name HA or name HB2 or name HB3)) or resid 412 through 508 or re \ sid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 13 through 479) selection = (chain 'E' and (resid 13 through 166 or (resid 167 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 479)) selection = (chain 'F' and resid 13 through 479) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 11.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.850 Extract box with map and model: 1.780 Check model and map are aligned: 0.360 Set scattering table: 0.430 Process input model: 103.990 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.006 0.074 30765 Z= 0.390 Angle : 0.679 23.922 41597 Z= 0.430 Chirality : 0.044 0.191 4824 Planarity : 0.004 0.068 5364 Dihedral : 15.442 152.429 11687 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3894 helix: 0.50 (0.13), residues: 1732 sheet: -1.58 (0.21), residues: 605 loop : -1.23 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 33 HIS 0.010 0.001 HIS E 371 PHE 0.028 0.001 PHE H 20 TYR 0.023 0.002 TYR h 18 ARG 0.021 0.001 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 3.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.8010 (p0) cc_final: 0.7653 (p0) REVERT: B 381 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7578 (ttm170) REVERT: B 455 LYS cc_start: 0.8324 (pttt) cc_final: 0.8052 (pttp) REVERT: C 50 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7206 (mt-10) REVERT: D 100 ASN cc_start: 0.8396 (m110) cc_final: 0.8004 (m110) REVERT: E 319 ASP cc_start: 0.7688 (t0) cc_final: 0.7311 (t0) REVERT: E 399 GLU cc_start: 0.7875 (tp30) cc_final: 0.7631 (tp30) REVERT: H 95 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7599 (tm-30) REVERT: J 39 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8100 (ttpt) REVERT: b 117 LEU cc_start: 0.7160 (tt) cc_final: 0.6935 (mm) REVERT: b 146 ARG cc_start: 0.6672 (ttt180) cc_final: 0.6432 (ttt180) REVERT: b 157 TYR cc_start: 0.6884 (t80) cc_final: 0.6630 (t80) REVERT: h 16 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7868 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.9482 time to fit residues: 636.1614 Evaluate side-chains 400 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30765 Z= 0.311 Angle : 0.581 6.600 41597 Z= 0.305 Chirality : 0.043 0.168 4824 Planarity : 0.004 0.063 5364 Dihedral : 6.885 135.553 4380 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.19 % Allowed : 5.18 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3894 helix: 0.79 (0.12), residues: 1751 sheet: -1.67 (0.21), residues: 593 loop : -1.27 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 33 HIS 0.007 0.001 HIS E 371 PHE 0.018 0.001 PHE J 34 TYR 0.017 0.001 TYR S 59 ARG 0.004 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 411 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 381 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7584 (ttm170) REVERT: B 455 LYS cc_start: 0.8327 (pttt) cc_final: 0.8045 (pttp) REVERT: C 224 ASP cc_start: 0.7925 (t0) cc_final: 0.7699 (t0) REVERT: D 100 ASN cc_start: 0.8284 (m110) cc_final: 0.7846 (m110) REVERT: E 315 TYR cc_start: 0.8859 (t80) cc_final: 0.8317 (t80) REVERT: E 319 ASP cc_start: 0.7764 (t0) cc_final: 0.7401 (t0) REVERT: E 397 MET cc_start: 0.7152 (tpt) cc_final: 0.6559 (tpt) REVERT: H 95 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7663 (tm-30) REVERT: H 132 GLN cc_start: 0.8013 (pp30) cc_final: 0.7719 (pt0) REVERT: J 39 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8075 (ttpt) REVERT: b 117 LEU cc_start: 0.7031 (tt) cc_final: 0.6736 (mm) REVERT: b 146 ARG cc_start: 0.6619 (ttt180) cc_final: 0.6326 (ttt180) REVERT: b 154 ARG cc_start: 0.6676 (mmm160) cc_final: 0.6001 (mmt90) REVERT: b 157 TYR cc_start: 0.6882 (t80) cc_final: 0.6632 (t80) REVERT: h 16 ARG cc_start: 0.8147 (ttp-170) cc_final: 0.7930 (ttp-170) outliers start: 6 outliers final: 5 residues processed: 414 average time/residue: 0.9878 time to fit residues: 622.6596 Evaluate side-chains 396 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 391 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain d residue 39 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 290 optimal weight: 0.8980 chunk 237 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 0.3980 chunk 280 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN F 267 GLN F 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30765 Z= 0.168 Angle : 0.509 5.666 41597 Z= 0.263 Chirality : 0.041 0.149 4824 Planarity : 0.004 0.051 5364 Dihedral : 6.418 107.559 4380 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.43 % Allowed : 6.33 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3894 helix: 1.20 (0.13), residues: 1756 sheet: -1.66 (0.21), residues: 574 loop : -1.10 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 33 HIS 0.005 0.001 HIS C 476 PHE 0.013 0.001 PHE J 34 TYR 0.014 0.001 TYR S 59 ARG 0.005 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 437 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 423 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 381 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7599 (ttm170) REVERT: B 455 LYS cc_start: 0.8331 (pttt) cc_final: 0.8002 (pttp) REVERT: C 54 GLU cc_start: 0.7276 (tt0) cc_final: 0.7049 (tt0) REVERT: C 224 ASP cc_start: 0.7908 (t0) cc_final: 0.7599 (t0) REVERT: D 100 ASN cc_start: 0.8209 (m110) cc_final: 0.7814 (m110) REVERT: E 319 ASP cc_start: 0.7798 (t0) cc_final: 0.7414 (t0) REVERT: E 397 MET cc_start: 0.7014 (tpt) cc_final: 0.6656 (tpt) REVERT: F 398 ASP cc_start: 0.7212 (m-30) cc_final: 0.6805 (m-30) REVERT: G 124 PHE cc_start: 0.8286 (m-10) cc_final: 0.7973 (m-10) REVERT: H 132 GLN cc_start: 0.8086 (pp30) cc_final: 0.7871 (pt0) REVERT: J 39 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8068 (ttpt) REVERT: b 117 LEU cc_start: 0.6778 (tt) cc_final: 0.6508 (mm) REVERT: b 146 ARG cc_start: 0.6553 (ttt180) cc_final: 0.6288 (ttt180) REVERT: b 154 ARG cc_start: 0.6518 (mmm160) cc_final: 0.6034 (mmt90) REVERT: d 95 GLU cc_start: 0.6001 (tm-30) cc_final: 0.5784 (tm-30) REVERT: d 138 VAL cc_start: 0.7309 (m) cc_final: 0.6950 (p) REVERT: h 16 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7912 (ttp-170) outliers start: 14 outliers final: 9 residues processed: 430 average time/residue: 0.9350 time to fit residues: 615.9509 Evaluate side-chains 400 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 391 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 350 optimal weight: 8.9990 chunk 371 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30765 Z= 0.201 Angle : 0.507 5.720 41597 Z= 0.262 Chirality : 0.041 0.144 4824 Planarity : 0.003 0.045 5364 Dihedral : 6.174 89.120 4380 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.43 % Allowed : 7.76 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3894 helix: 1.35 (0.13), residues: 1755 sheet: -1.71 (0.21), residues: 584 loop : -1.03 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 33 HIS 0.005 0.001 HIS E 371 PHE 0.014 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.006 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 404 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7567 (t0) cc_final: 0.7362 (t0) REVERT: B 381 ARG cc_start: 0.7986 (mmm-85) cc_final: 0.7628 (ttm-80) REVERT: B 455 LYS cc_start: 0.8359 (pttt) cc_final: 0.8021 (pttp) REVERT: C 224 ASP cc_start: 0.7945 (t0) cc_final: 0.7599 (t0) REVERT: D 100 ASN cc_start: 0.8246 (m110) cc_final: 0.7820 (m110) REVERT: E 319 ASP cc_start: 0.7815 (t0) cc_final: 0.7422 (t0) REVERT: E 397 MET cc_start: 0.7034 (tpt) cc_final: 0.6423 (tpt) REVERT: F 398 ASP cc_start: 0.7235 (m-30) cc_final: 0.6804 (m-30) REVERT: G 124 PHE cc_start: 0.8308 (m-10) cc_final: 0.7998 (m-10) REVERT: I 20 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7714 (mtmt) REVERT: J 39 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8098 (ttpt) REVERT: b 117 LEU cc_start: 0.6757 (tt) cc_final: 0.6488 (mm) REVERT: b 154 ARG cc_start: 0.6563 (mmm160) cc_final: 0.6069 (mmt90) outliers start: 14 outliers final: 13 residues processed: 410 average time/residue: 0.9801 time to fit residues: 614.1242 Evaluate side-chains 405 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 392 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 475 GLN F 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30765 Z= 0.252 Angle : 0.515 5.757 41597 Z= 0.266 Chirality : 0.041 0.144 4824 Planarity : 0.004 0.050 5364 Dihedral : 6.094 89.668 4380 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.43 % Allowed : 8.63 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3894 helix: 1.38 (0.13), residues: 1754 sheet: -1.74 (0.21), residues: 576 loop : -1.04 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 4 HIS 0.006 0.001 HIS E 371 PHE 0.016 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.005 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 396 time to evaluate : 3.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7600 (t0) cc_final: 0.7391 (t0) REVERT: B 381 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7683 (ttm-80) REVERT: B 455 LYS cc_start: 0.8358 (pttt) cc_final: 0.8019 (pttp) REVERT: C 54 GLU cc_start: 0.7303 (tt0) cc_final: 0.7083 (tt0) REVERT: C 224 ASP cc_start: 0.7983 (t0) cc_final: 0.7635 (t0) REVERT: D 100 ASN cc_start: 0.8289 (m110) cc_final: 0.7829 (m110) REVERT: D 362 MET cc_start: 0.8857 (tpt) cc_final: 0.8424 (tpt) REVERT: E 319 ASP cc_start: 0.7790 (t0) cc_final: 0.7392 (t0) REVERT: E 397 MET cc_start: 0.6986 (tpt) cc_final: 0.6388 (tpt) REVERT: F 398 ASP cc_start: 0.7263 (m-30) cc_final: 0.6799 (m-30) REVERT: G 124 PHE cc_start: 0.8357 (m-10) cc_final: 0.8037 (m-10) REVERT: H 135 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7889 (mp) REVERT: J 39 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8110 (ttpt) REVERT: b 117 LEU cc_start: 0.6841 (tt) cc_final: 0.6570 (mm) REVERT: b 154 ARG cc_start: 0.6408 (mmm160) cc_final: 0.5984 (mmt90) outliers start: 14 outliers final: 13 residues processed: 402 average time/residue: 0.9643 time to fit residues: 595.4738 Evaluate side-chains 402 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 388 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 10.0000 chunk 308 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN F 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 30765 Z= 0.367 Angle : 0.552 6.144 41597 Z= 0.287 Chirality : 0.043 0.145 4824 Planarity : 0.004 0.056 5364 Dihedral : 6.234 86.644 4380 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.59 % Allowed : 9.62 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3894 helix: 1.28 (0.12), residues: 1748 sheet: -1.90 (0.21), residues: 590 loop : -1.06 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 33 HIS 0.008 0.001 HIS E 371 PHE 0.020 0.001 PHE J 34 TYR 0.015 0.002 TYR S 59 ARG 0.007 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 392 time to evaluate : 3.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7633 (t0) cc_final: 0.7421 (t0) REVERT: B 381 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7659 (ttm-80) REVERT: B 455 LYS cc_start: 0.8351 (pttt) cc_final: 0.8075 (pttp) REVERT: C 224 ASP cc_start: 0.8027 (t0) cc_final: 0.7695 (t0) REVERT: D 362 MET cc_start: 0.8882 (tpt) cc_final: 0.8429 (tpt) REVERT: E 319 ASP cc_start: 0.7799 (t0) cc_final: 0.7391 (t0) REVERT: E 397 MET cc_start: 0.6960 (tpt) cc_final: 0.6367 (tpt) REVERT: F 190 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9116 (p) REVERT: G 124 PHE cc_start: 0.8433 (m-10) cc_final: 0.8076 (m-10) REVERT: H 135 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7962 (mp) REVERT: J 39 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8113 (ttpt) REVERT: S 184 ARG cc_start: 0.8313 (ttm110) cc_final: 0.7889 (mtm110) REVERT: b 117 LEU cc_start: 0.6951 (tt) cc_final: 0.6676 (mm) REVERT: b 154 ARG cc_start: 0.6541 (mmm160) cc_final: 0.6088 (mmt90) outliers start: 19 outliers final: 15 residues processed: 402 average time/residue: 1.0094 time to fit residues: 623.5559 Evaluate side-chains 405 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 388 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 271 optimal weight: 0.4980 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 297 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30765 Z= 0.241 Angle : 0.516 7.118 41597 Z= 0.266 Chirality : 0.041 0.145 4824 Planarity : 0.004 0.058 5364 Dihedral : 6.086 89.473 4380 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.62 % Allowed : 9.78 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3894 helix: 1.40 (0.12), residues: 1765 sheet: -1.81 (0.21), residues: 576 loop : -1.05 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 4 HIS 0.005 0.001 HIS E 371 PHE 0.017 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.009 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 400 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7696 (t0) cc_final: 0.7469 (t0) REVERT: B 381 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7646 (ttm-80) REVERT: B 455 LYS cc_start: 0.8355 (pttt) cc_final: 0.8076 (pttp) REVERT: B 477 GLN cc_start: 0.8372 (mm110) cc_final: 0.8141 (tp40) REVERT: C 224 ASP cc_start: 0.8015 (t0) cc_final: 0.7677 (t0) REVERT: C 381 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7291 (ttt90) REVERT: D 362 MET cc_start: 0.8845 (tpt) cc_final: 0.8404 (tpt) REVERT: E 312 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: E 319 ASP cc_start: 0.7800 (t0) cc_final: 0.7397 (t0) REVERT: E 397 MET cc_start: 0.6971 (tpt) cc_final: 0.6387 (tpt) REVERT: F 190 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.9065 (p) REVERT: G 124 PHE cc_start: 0.8366 (m-10) cc_final: 0.8046 (m-10) REVERT: H 135 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7940 (mp) REVERT: J 39 LYS cc_start: 0.8344 (ttpp) cc_final: 0.8115 (ttpt) REVERT: J 41 GLN cc_start: 0.7940 (mt0) cc_final: 0.7713 (mt0) REVERT: S 184 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7846 (mtm110) REVERT: b 117 LEU cc_start: 0.6951 (tt) cc_final: 0.6672 (mm) REVERT: b 154 ARG cc_start: 0.6481 (mmm160) cc_final: 0.6086 (mmt90) outliers start: 20 outliers final: 17 residues processed: 411 average time/residue: 0.9497 time to fit residues: 596.1197 Evaluate side-chains 411 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 391 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 GLN F 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30765 Z= 0.224 Angle : 0.508 7.871 41597 Z= 0.261 Chirality : 0.041 0.143 4824 Planarity : 0.003 0.064 5364 Dihedral : 5.976 89.733 4380 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.62 % Allowed : 10.02 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3894 helix: 1.51 (0.13), residues: 1761 sheet: -1.80 (0.21), residues: 576 loop : -1.01 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.005 0.001 HIS E 371 PHE 0.015 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.010 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 401 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7727 (t0) cc_final: 0.7482 (t0) REVERT: B 381 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7637 (ttm-80) REVERT: B 455 LYS cc_start: 0.8376 (pttt) cc_final: 0.8098 (pttp) REVERT: C 54 GLU cc_start: 0.7450 (tt0) cc_final: 0.7246 (tt0) REVERT: C 224 ASP cc_start: 0.8001 (t0) cc_final: 0.7648 (t0) REVERT: C 381 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7309 (ttt90) REVERT: D 362 MET cc_start: 0.8850 (tpt) cc_final: 0.8423 (tpt) REVERT: E 312 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.7751 (mp-120) REVERT: E 319 ASP cc_start: 0.7804 (t0) cc_final: 0.7402 (t0) REVERT: E 397 MET cc_start: 0.6958 (tpt) cc_final: 0.6380 (tpt) REVERT: F 190 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9083 (p) REVERT: G 124 PHE cc_start: 0.8360 (m-10) cc_final: 0.8008 (m-10) REVERT: H 135 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mp) REVERT: J 39 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8112 (ttpt) REVERT: J 41 GLN cc_start: 0.7934 (mt0) cc_final: 0.7708 (mt0) REVERT: S 184 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7871 (mtm110) REVERT: b 117 LEU cc_start: 0.6841 (tt) cc_final: 0.6586 (mm) REVERT: b 154 ARG cc_start: 0.6464 (mmm160) cc_final: 0.6058 (mmt90) outliers start: 20 outliers final: 16 residues processed: 413 average time/residue: 0.9563 time to fit residues: 603.1932 Evaluate side-chains 410 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 391 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 343 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30765 Z= 0.332 Angle : 0.539 7.600 41597 Z= 0.279 Chirality : 0.042 0.146 4824 Planarity : 0.004 0.067 5364 Dihedral : 6.125 88.107 4380 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.71 % Allowed : 10.06 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3894 helix: 1.41 (0.12), residues: 1764 sheet: -1.88 (0.21), residues: 578 loop : -1.07 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 33 HIS 0.007 0.001 HIS E 371 PHE 0.019 0.001 PHE J 34 TYR 0.014 0.001 TYR S 59 ARG 0.011 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 419 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 396 time to evaluate : 3.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7767 (t0) cc_final: 0.7526 (t0) REVERT: B 381 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7686 (ttm-80) REVERT: B 455 LYS cc_start: 0.8370 (pttt) cc_final: 0.8092 (pttp) REVERT: C 224 ASP cc_start: 0.7998 (t0) cc_final: 0.7659 (t0) REVERT: C 381 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7369 (ttt90) REVERT: D 362 MET cc_start: 0.8868 (tpt) cc_final: 0.8432 (tpt) REVERT: E 312 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.7754 (mp-120) REVERT: E 319 ASP cc_start: 0.7810 (t0) cc_final: 0.7404 (t0) REVERT: E 397 MET cc_start: 0.6962 (tpt) cc_final: 0.6385 (tpt) REVERT: F 190 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9113 (p) REVERT: G 124 PHE cc_start: 0.8372 (m-10) cc_final: 0.8011 (m-10) REVERT: H 135 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7944 (mp) REVERT: I 24 ASP cc_start: 0.7892 (p0) cc_final: 0.7673 (p0) REVERT: J 39 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8115 (ttpt) REVERT: S 51 MET cc_start: 0.7566 (tpt) cc_final: 0.7164 (tpt) REVERT: S 184 ARG cc_start: 0.8308 (ttm110) cc_final: 0.7831 (mtm110) REVERT: b 117 LEU cc_start: 0.6963 (tt) cc_final: 0.6705 (mm) REVERT: b 154 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6079 (mmt90) outliers start: 23 outliers final: 18 residues processed: 408 average time/residue: 0.9947 time to fit residues: 620.1175 Evaluate side-chains 413 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 392 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30765 Z= 0.269 Angle : 0.526 8.253 41597 Z= 0.271 Chirality : 0.042 0.145 4824 Planarity : 0.004 0.071 5364 Dihedral : 6.084 89.904 4380 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.56 % Allowed : 10.40 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3894 helix: 1.45 (0.12), residues: 1764 sheet: -1.85 (0.21), residues: 576 loop : -1.05 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 33 HIS 0.006 0.001 HIS E 371 PHE 0.017 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.012 0.000 ARG b 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 390 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 224 ASP cc_start: 0.7772 (t0) cc_final: 0.7530 (t0) REVERT: B 381 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7643 (ttm-80) REVERT: B 455 LYS cc_start: 0.8371 (pttt) cc_final: 0.8095 (pttp) REVERT: C 54 GLU cc_start: 0.7370 (tt0) cc_final: 0.7150 (tt0) REVERT: C 224 ASP cc_start: 0.7998 (t0) cc_final: 0.7662 (t0) REVERT: C 381 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7302 (ttt90) REVERT: D 362 MET cc_start: 0.8865 (tpt) cc_final: 0.8434 (tpt) REVERT: D 432 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8483 (mp) REVERT: E 312 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.7744 (mp-120) REVERT: E 319 ASP cc_start: 0.7806 (t0) cc_final: 0.7406 (t0) REVERT: E 397 MET cc_start: 0.6915 (tpt) cc_final: 0.6352 (tpt) REVERT: F 190 VAL cc_start: 0.9326 (OUTLIER) cc_final: 0.9087 (p) REVERT: G 124 PHE cc_start: 0.8371 (m-10) cc_final: 0.8007 (m-10) REVERT: H 135 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7935 (mp) REVERT: J 39 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8109 (ttpt) REVERT: S 51 MET cc_start: 0.7565 (tpt) cc_final: 0.7164 (tpt) REVERT: S 184 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7857 (mtm110) REVERT: b 117 LEU cc_start: 0.6897 (tt) cc_final: 0.6648 (mm) REVERT: b 154 ARG cc_start: 0.6459 (mmm160) cc_final: 0.6049 (mmt90) outliers start: 18 outliers final: 14 residues processed: 400 average time/residue: 0.9722 time to fit residues: 594.3559 Evaluate side-chains 404 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 386 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain G residue 233 ASP Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain b residue 83 ASP Chi-restraints excluded: chain b residue 198 ILE Chi-restraints excluded: chain d residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.8980 chunk 324 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 431 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.128853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098181 restraints weight = 117463.919| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.42 r_work: 0.2869 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30765 Z= 0.265 Angle : 0.521 8.247 41597 Z= 0.269 Chirality : 0.042 0.143 4824 Planarity : 0.004 0.071 5364 Dihedral : 6.022 89.609 4380 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.62 % Allowed : 10.37 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3894 helix: 1.50 (0.12), residues: 1763 sheet: -1.84 (0.21), residues: 576 loop : -1.04 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 4 HIS 0.006 0.001 HIS E 371 PHE 0.017 0.001 PHE J 34 TYR 0.013 0.001 TYR S 59 ARG 0.011 0.000 ARG b 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13189.17 seconds wall clock time: 226 minutes 2.49 seconds (13562.49 seconds total)