Starting phenix.real_space_refine on Sat May 24 04:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi2_60119/05_2025/8zi2_60119.cif" } resolution = 2.99 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 4 5.21 5 S 99 5.16 5 C 15720 2.51 5 N 4294 2.21 5 O 4881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25009 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3702 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "B" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 471} Chain: "C" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3703 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 471} Chain: "D" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "E" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3525 Classifications: {'peptide': 463} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 440} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 959 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "g" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2243 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 279} 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} Time building chain proxies: 14.19, per 1000 atoms: 0.57 Number of scatterers: 25009 At special positions: 0 Unit cell: (140.712, 139.854, 147.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 11 15.00 Mg 4 11.99 O 4881 8.00 N 4294 7.00 C 15720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 3.5 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5958 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 27 sheets defined 45.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.561A pdb=" N MET A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 220 removed outlier: 3.626A pdb=" N ALA A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 220' Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.542A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.965A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.857A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 340 through 348 removed outlier: 3.671A pdb=" N THR A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 384 through 404 removed outlier: 3.828A pdb=" N LEU A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 455 through 458 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 479 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 494 through 512 removed outlier: 3.935A pdb=" N ALA A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 512 " --> pdb=" O PHE A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.045A pdb=" N SER B 82 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.785A pdb=" N LEU B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.724A pdb=" N MET B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.588A pdb=" N SER B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.541A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.507A pdb=" N SER B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 Processing helix chain 'B' and resid 378 through 383 removed outlier: 3.939A pdb=" N SER B 381 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 383 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 391 Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.691A pdb=" N ARG B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.515A pdb=" N GLY B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 480 Processing helix chain 'B' and resid 480 through 490 Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.618A pdb=" N MET C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.979A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE C 250 " --> pdb=" O MET C 246 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 removed outlier: 4.163A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 removed outlier: 3.941A pdb=" N LEU C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 299 " --> pdb=" O HIS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 363 Processing helix chain 'C' and resid 378 through 382 removed outlier: 4.020A pdb=" N SER C 381 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 382 " --> pdb=" O GLY C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 382' Processing helix chain 'C' and resid 384 through 391 Processing helix chain 'C' and resid 394 through 409 Processing helix chain 'C' and resid 415 through 432 Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.786A pdb=" N ALA C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 Processing helix chain 'C' and resid 494 through 510 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.836A pdb=" N THR D 82 " --> pdb=" O GLY D 79 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 83 " --> pdb=" O THR D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 83' Processing helix chain 'D' and resid 129 through 136 removed outlier: 3.549A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 211 through 217 removed outlier: 3.555A pdb=" N ARG D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG D 217 " --> pdb=" O GLY D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 232 removed outlier: 3.826A pdb=" N THR D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 229 " --> pdb=" O MET D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 removed outlier: 4.083A pdb=" N TYR D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.904A pdb=" N LEU D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 307 Processing helix chain 'D' and resid 310 through 317 removed outlier: 3.922A pdb=" N THR D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 356 through 373 Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 388 through 405 removed outlier: 3.800A pdb=" N VAL D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 4.412A pdb=" N THR D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 437 Processing helix chain 'D' and resid 444 through 448 removed outlier: 3.523A pdb=" N PHE D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 464 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.657A pdb=" N GLN E 118 " --> pdb=" O TYR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 153 through 170 removed outlier: 4.218A pdb=" N ASN E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 166 " --> pdb=" O ILE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 211 through 216 Processing helix chain 'E' and resid 217 through 232 removed outlier: 3.893A pdb=" N THR E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 263 removed outlier: 3.834A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 287 removed outlier: 3.910A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 319 removed outlier: 3.543A pdb=" N ALA E 318 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 334 Processing helix chain 'E' and resid 355 through 383 removed outlier: 3.601A pdb=" N VAL E 365 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN E 366 " --> pdb=" O ALA E 362 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 405 removed outlier: 3.690A pdb=" N VAL E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 453 through 464 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.828A pdb=" N THR F 82 " --> pdb=" O GLY F 79 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 83 " --> pdb=" O THR F 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 79 through 83' Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 153 through 170 removed outlier: 3.644A pdb=" N ALA F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 211 through 217 removed outlier: 3.624A pdb=" N ARG F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG F 217 " --> pdb=" O GLY F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 231 removed outlier: 3.636A pdb=" N MET F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.669A pdb=" N TYR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 286 removed outlier: 4.349A pdb=" N ARG F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.610A pdb=" N ASP F 306 " --> pdb=" O VAL F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 removed outlier: 3.779A pdb=" N ALA F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 334 Processing helix chain 'F' and resid 355 through 382 removed outlier: 4.372A pdb=" N ASP F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 405 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 424 through 438 Processing helix chain 'F' and resid 444 through 449 removed outlier: 3.782A pdb=" N TYR F 449 " --> pdb=" O GLN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 464 removed outlier: 3.665A pdb=" N ILE F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 106 removed outlier: 4.372A pdb=" N GLU e 102 " --> pdb=" O ARG e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 112 Processing helix chain 'e' and resid 119 through 132 Processing helix chain 'g' and resid 3 through 60 Proline residue: g 44 - end of helix Processing helix chain 'g' and resid 65 through 69 Processing helix chain 'g' and resid 90 through 109 Processing helix chain 'g' and resid 119 through 130 Processing helix chain 'g' and resid 145 through 148 Processing helix chain 'g' and resid 149 through 162 removed outlier: 4.077A pdb=" N VAL g 153 " --> pdb=" O LEU g 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 216 through 289 removed outlier: 4.078A pdb=" N GLY g 220 " --> pdb=" O GLU g 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 4.022A pdb=" N MET A 34 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE A 61 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.576A pdb=" N LEU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.888A pdb=" N ARG A 107 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.679A pdb=" N VAL A 160 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 330 through 332 removed outlier: 6.788A pdb=" N ILE A 168 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 167 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 356 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 169 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.817A pdb=" N MET B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 61 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 54 removed outlier: 5.317A pdb=" N ARG B 94 " --> pdb=" O MET B 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.632A pdb=" N VAL F 67 " --> pdb=" O GLY F 4 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG F 51 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN F 44 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL F 49 " --> pdb=" O GLN F 44 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.025A pdb=" N LEU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.545A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 228 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 193 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 261 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 323 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.545A pdb=" N VAL B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 228 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS B 194 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA B 198 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 193 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR B 261 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE B 168 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 167 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 removed outlier: 4.589A pdb=" N VAL B 160 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 36 removed outlier: 3.811A pdb=" N MET C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN C 66 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU C 77 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY C 62 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE C 54 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 64 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU C 52 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N MET C 53 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 92 " --> pdb=" O MET C 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.882A pdb=" N LEU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.960A pdb=" N ARG C 107 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS C 194 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 227 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ALA C 198 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR C 261 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE C 168 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 167 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 10 removed outlier: 5.982A pdb=" N ILE D 6 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU D 17 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 15 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL D 49 " --> pdb=" O GLN D 44 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLN D 44 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG D 51 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR D 38 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 87 removed outlier: 3.669A pdb=" N ALA D 202 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 144 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL D 301 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU D 146 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR D 345 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 10 removed outlier: 4.202A pdb=" N ARG E 5 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E 13 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE E 53 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL E 41 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 67 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 75 through 77 Processing sheet with id=AC3, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.604A pdb=" N VAL E 174 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL E 242 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE E 298 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU E 244 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA E 300 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL E 246 " --> pdb=" O ALA E 300 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 75 through 77 Processing sheet with id=AC5, first strand: chain 'F' and resid 86 through 87 removed outlier: 7.170A pdb=" N SER F 173 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL F 204 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE F 175 " --> pdb=" O VAL F 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 86 through 87 removed outlier: 7.170A pdb=" N SER F 173 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL F 204 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE F 175 " --> pdb=" O VAL F 204 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE F 298 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU F 244 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA F 300 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL F 246 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 322 " --> pdb=" O LYS F 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 15 through 17 removed outlier: 3.583A pdb=" N ILE e 15 " --> pdb=" O VAL e 8 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS e 6 " --> pdb=" O SER e 17 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP e 7 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA e 80 " --> pdb=" O ASP e 7 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY e 67 " --> pdb=" O LEU e 45 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU e 69 " --> pdb=" O THR e 43 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR e 43 " --> pdb=" O LEU e 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'g' and resid 133 through 136 removed outlier: 6.527A pdb=" N PHE g 115 " --> pdb=" O VAL g 133 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLY g 135 " --> pdb=" O PHE g 115 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU g 117 " --> pdb=" O GLY g 135 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TYR g 169 " --> pdb=" O GLY g 77 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE g 79 " --> pdb=" O TYR g 169 " (cutoff:3.500A) 1131 hydrogen bonds defined for protein. 3267 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: 9.12 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4499 1.32 - 1.44: 5955 1.44 - 1.57: 14735 1.57 - 1.69: 17 1.69 - 1.81: 184 Bond restraints: 25390 Sorted by residual: bond pdb=" N LEU B 278 " pdb=" CA LEU B 278 " ideal model delta sigma weight residual 1.457 1.508 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER F 121 " pdb=" C SER F 121 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" N ILE D 249 " pdb=" CA ILE D 249 " ideal model delta sigma weight residual 1.460 1.501 -0.042 1.21e-02 6.83e+03 1.19e+01 bond pdb=" N VAL E 201 " pdb=" CA VAL E 201 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N GLU B 55 " pdb=" CA GLU B 55 " ideal model delta sigma weight residual 1.458 1.500 -0.043 1.27e-02 6.20e+03 1.12e+01 ... (remaining 25385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 32934 2.06 - 4.13: 1304 4.13 - 6.19: 153 6.19 - 8.25: 15 8.25 - 10.32: 6 Bond angle restraints: 34412 Sorted by residual: angle pdb=" N VAL F 451 " pdb=" CA VAL F 451 " pdb=" C VAL F 451 " ideal model delta sigma weight residual 112.43 116.11 -3.68 9.20e-01 1.18e+00 1.60e+01 angle pdb=" N LEU B 277 " pdb=" CA LEU B 277 " pdb=" C LEU B 277 " ideal model delta sigma weight residual 112.23 107.20 5.03 1.26e+00 6.30e-01 1.59e+01 angle pdb=" N ASN A 28 " pdb=" CA ASN A 28 " pdb=" C ASN A 28 " ideal model delta sigma weight residual 113.88 108.98 4.90 1.23e+00 6.61e-01 1.59e+01 angle pdb=" N ALA A 46 " pdb=" CA ALA A 46 " pdb=" C ALA A 46 " ideal model delta sigma weight residual 111.28 115.62 -4.34 1.09e+00 8.42e-01 1.58e+01 angle pdb=" N TYR D 189 " pdb=" CA TYR D 189 " pdb=" C TYR D 189 " ideal model delta sigma weight residual 111.33 106.52 4.81 1.21e+00 6.83e-01 1.58e+01 ... (remaining 34407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 14146 17.77 - 35.54: 1026 35.54 - 53.31: 213 53.31 - 71.08: 86 71.08 - 88.85: 14 Dihedral angle restraints: 15485 sinusoidal: 6134 harmonic: 9351 Sorted by residual: dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 10.64 -70.64 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA ILE B 54 " pdb=" C ILE B 54 " pdb=" N GLU B 55 " pdb=" CA GLU B 55 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO g 190 " pdb=" C PRO g 190 " pdb=" N LEU g 191 " pdb=" CA LEU g 191 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 15482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2860 0.049 - 0.098: 791 0.098 - 0.147: 282 0.147 - 0.197: 32 0.197 - 0.246: 10 Chirality restraints: 3975 Sorted by residual: chirality pdb=" CA ILE E 287 " pdb=" N ILE E 287 " pdb=" C ILE E 287 " pdb=" CB ILE E 287 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN e 56 " pdb=" N ASN e 56 " pdb=" C ASN e 56 " pdb=" CB ASN e 56 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL e 68 " pdb=" N VAL e 68 " pdb=" C VAL e 68 " pdb=" CB VAL e 68 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3972 not shown) Planarity restraints: 4484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 106 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C ALA e 106 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA e 106 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN e 107 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 246 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C VAL D 246 " -0.046 2.00e-02 2.50e+03 pdb=" O VAL D 246 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 247 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 310 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO E 311 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " 0.036 5.00e-02 4.00e+02 ... (remaining 4481 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 63 2.45 - 3.07: 17358 3.07 - 3.68: 36199 3.68 - 4.29: 52570 4.29 - 4.90: 89258 Nonbonded interactions: 195448 Sorted by model distance: nonbonded pdb=" O1B ATP B 601 " pdb="MG MG B 602 " model vdw 1.843 2.170 nonbonded pdb=" O3G ATP B 601 " pdb="MG MG B 602 " model vdw 1.917 2.170 nonbonded pdb=" O3G ATP A 601 " pdb="MG MG A 602 " model vdw 1.938 2.170 nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 1.947 2.170 nonbonded pdb="MG MG C 601 " pdb=" O3G ATP C 602 " model vdw 2.022 2.170 ... (remaining 195443 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 26 through 514) selection = (chain 'B' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) selection = (chain 'C' and (resid 26 through 513 or (resid 514 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )))) } ncs_group { reference = (chain 'D' and resid 2 through 464) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 53.970 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 0.070 25390 Z= 0.393 Angle : 0.864 10.317 34412 Z= 0.562 Chirality : 0.052 0.246 3975 Planarity : 0.005 0.089 4484 Dihedral : 13.783 88.855 9527 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3260 helix: 1.16 (0.15), residues: 1232 sheet: 0.21 (0.25), residues: 427 loop : -1.35 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP g 206 HIS 0.005 0.001 HIS C 43 PHE 0.018 0.001 PHE D 175 TYR 0.018 0.001 TYR D 205 ARG 0.014 0.001 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.20404 ( 1118) hydrogen bonds : angle 7.45643 ( 3267) covalent geometry : bond 0.00612 (25390) covalent geometry : angle 0.86380 (34412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 208 MET cc_start: 0.7841 (mtp) cc_final: 0.7640 (mtt) REVERT: F 254 LEU cc_start: 0.8195 (mt) cc_final: 0.7993 (mt) REVERT: e 59 GLU cc_start: 0.6407 (tm-30) cc_final: 0.6042 (tm-30) REVERT: e 60 GLU cc_start: 0.3359 (pm20) cc_final: 0.1115 (tt0) REVERT: g 166 ASP cc_start: 0.3115 (m-30) cc_final: 0.2881 (m-30) REVERT: g 225 TYR cc_start: 0.8728 (t80) cc_final: 0.8429 (t80) REVERT: g 227 GLU cc_start: 0.9173 (pt0) cc_final: 0.8887 (pp20) outliers start: 0 outliers final: 1 residues processed: 336 average time/residue: 1.4515 time to fit residues: 555.6748 Evaluate side-chains 181 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 384 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 293 optimal weight: 30.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN D 44 GLN D 209 ASN E 31 GLN E 186 ASN g 148 GLN ** g 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.115339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084997 restraints weight = 52442.800| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.19 r_work: 0.3168 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 25390 Z= 0.203 Angle : 0.645 13.948 34412 Z= 0.344 Chirality : 0.046 0.164 3975 Planarity : 0.005 0.062 4484 Dihedral : 6.928 84.579 3686 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.20 % Allowed : 14.45 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3260 helix: 1.19 (0.15), residues: 1277 sheet: 0.34 (0.25), residues: 437 loop : -1.35 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 139 HIS 0.005 0.001 HIS F 190 PHE 0.015 0.002 PHE A 410 TYR 0.026 0.002 TYR g 169 ARG 0.011 0.001 ARG D 105 Details of bonding type rmsd hydrogen bonds : bond 0.05494 ( 1118) hydrogen bonds : angle 5.47355 ( 3267) covalent geometry : bond 0.00479 (25390) covalent geometry : angle 0.64524 (34412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 190 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: A 238 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7042 (tm) REVERT: A 505 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7964 (pp) REVERT: B 53 MET cc_start: 0.8084 (mtm) cc_final: 0.7470 (mmt) REVERT: B 246 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7453 (mtt) REVERT: D 87 MET cc_start: 0.8932 (mtp) cc_final: 0.8588 (mtp) REVERT: D 225 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7697 (mtt) REVERT: F 203 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8232 (mtp) REVERT: g 170 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9189 (mm) REVERT: g 188 LEU cc_start: 0.8712 (pp) cc_final: 0.8478 (pp) REVERT: g 232 GLN cc_start: 0.9145 (tp40) cc_final: 0.8903 (tm-30) REVERT: g 262 ASP cc_start: 0.8685 (t0) cc_final: 0.8416 (t0) outliers start: 84 outliers final: 32 residues processed: 248 average time/residue: 1.2417 time to fit residues: 361.3370 Evaluate side-chains 205 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 444 ASP Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain e residue 129 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 170 LEU Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 141 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 318 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 284 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN e 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.115707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085314 restraints weight = 51983.494| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.17 r_work: 0.3172 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25390 Z= 0.150 Angle : 0.566 12.844 34412 Z= 0.299 Chirality : 0.044 0.153 3975 Planarity : 0.004 0.057 4484 Dihedral : 6.569 85.165 3683 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.71 % Allowed : 15.68 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.15), residues: 3260 helix: 1.29 (0.15), residues: 1281 sheet: 0.34 (0.25), residues: 444 loop : -1.31 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS F 190 PHE 0.023 0.001 PHE g 125 TYR 0.015 0.001 TYR E 250 ARG 0.009 0.000 ARG E 251 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 1118) hydrogen bonds : angle 5.05540 ( 3267) covalent geometry : bond 0.00348 (25390) covalent geometry : angle 0.56628 (34412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7096 (tm) REVERT: A 469 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8597 (t0) REVERT: B 246 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7455 (mtt) REVERT: D 87 MET cc_start: 0.8900 (mtp) cc_final: 0.8625 (mtp) REVERT: D 159 MET cc_start: 0.8229 (mmm) cc_final: 0.7933 (mmp) REVERT: D 225 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7931 (mtt) REVERT: E 266 MET cc_start: 0.2025 (pmm) cc_final: 0.1742 (pmm) REVERT: g 26 MET cc_start: 0.8569 (mmt) cc_final: 0.8259 (mmt) REVERT: g 188 LEU cc_start: 0.8766 (pp) cc_final: 0.8527 (pp) outliers start: 71 outliers final: 31 residues processed: 234 average time/residue: 1.2701 time to fit residues: 347.6039 Evaluate side-chains 205 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 100 ASN Chi-restraints excluded: chain e residue 129 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 122 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 310 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 315 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN D 209 ASN E 248 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 ASN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.116499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.086014 restraints weight = 52525.623| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.22 r_work: 0.3185 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25390 Z= 0.120 Angle : 0.541 12.565 34412 Z= 0.281 Chirality : 0.043 0.181 3975 Planarity : 0.004 0.054 4484 Dihedral : 6.357 85.486 3683 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.17 % Allowed : 15.75 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.15), residues: 3260 helix: 1.37 (0.15), residues: 1287 sheet: 0.45 (0.25), residues: 441 loop : -1.25 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.006 0.001 HIS e 38 PHE 0.019 0.001 PHE g 125 TYR 0.014 0.001 TYR A 475 ARG 0.009 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 1118) hydrogen bonds : angle 4.79925 ( 3267) covalent geometry : bond 0.00270 (25390) covalent geometry : angle 0.54063 (34412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 194 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7107 (tm) REVERT: A 469 ASP cc_start: 0.8810 (t70) cc_final: 0.8605 (t0) REVERT: B 246 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7441 (mtt) REVERT: C 131 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: C 284 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7607 (ttt180) REVERT: C 334 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: D 87 MET cc_start: 0.8791 (mtp) cc_final: 0.8538 (mtp) REVERT: D 225 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7718 (mtt) REVERT: E 350 ASP cc_start: 0.8953 (t0) cc_final: 0.8663 (t0) REVERT: E 374 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8716 (mm-30) REVERT: F 92 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8326 (mtt-85) REVERT: g 26 MET cc_start: 0.8632 (mmt) cc_final: 0.8282 (mmt) REVERT: g 179 MET cc_start: 0.7609 (pmm) cc_final: 0.7324 (pmm) REVERT: g 232 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8883 (tm-30) outliers start: 83 outliers final: 38 residues processed: 255 average time/residue: 1.2562 time to fit residues: 374.8305 Evaluate side-chains 208 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 129 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 261 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 296 optimal weight: 0.6980 chunk 258 optimal weight: 0.6980 chunk 302 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN D 248 ASN E 284 GLN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN e 100 ASN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.118201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087583 restraints weight = 51859.251| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.22 r_work: 0.3212 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25390 Z= 0.104 Angle : 0.529 12.641 34412 Z= 0.273 Chirality : 0.043 0.168 3975 Planarity : 0.004 0.051 4484 Dihedral : 6.112 86.651 3683 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.97 % Allowed : 16.74 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3260 helix: 1.43 (0.15), residues: 1304 sheet: 0.75 (0.26), residues: 430 loop : -1.18 (0.15), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 139 HIS 0.004 0.001 HIS e 38 PHE 0.016 0.001 PHE g 125 TYR 0.020 0.001 TYR g 225 ARG 0.008 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 1118) hydrogen bonds : angle 4.59343 ( 3267) covalent geometry : bond 0.00224 (25390) covalent geometry : angle 0.52864 (34412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7082 (tm) REVERT: A 469 ASP cc_start: 0.8815 (t70) cc_final: 0.8603 (t0) REVERT: B 246 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7447 (mtt) REVERT: C 284 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7601 (ttt180) REVERT: D 87 MET cc_start: 0.8671 (mtp) cc_final: 0.8469 (mtp) REVERT: D 159 MET cc_start: 0.8193 (mmm) cc_final: 0.7883 (mmp) REVERT: D 225 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: E 350 ASP cc_start: 0.8862 (t0) cc_final: 0.8521 (t0) REVERT: E 374 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8773 (mm-30) REVERT: e 123 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: g 24 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7556 (mtp) REVERT: g 26 MET cc_start: 0.8708 (mmt) cc_final: 0.8344 (mmt) REVERT: g 179 MET cc_start: 0.7668 (pmm) cc_final: 0.7374 (pmm) REVERT: g 232 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8927 (tm-30) outliers start: 78 outliers final: 35 residues processed: 251 average time/residue: 1.2600 time to fit residues: 368.4636 Evaluate side-chains 212 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 123 GLU Chi-restraints excluded: chain e residue 129 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 231 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN E 8 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 100 ASN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 277 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084800 restraints weight = 52234.683| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.19 r_work: 0.3165 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25390 Z= 0.168 Angle : 0.569 12.409 34412 Z= 0.297 Chirality : 0.044 0.184 3975 Planarity : 0.004 0.048 4484 Dihedral : 6.207 85.500 3683 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.43 % Allowed : 17.12 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3260 helix: 1.38 (0.15), residues: 1296 sheet: 0.63 (0.25), residues: 442 loop : -1.24 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 139 HIS 0.005 0.001 HIS F 190 PHE 0.014 0.001 PHE g 125 TYR 0.014 0.001 TYR A 475 ARG 0.010 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 1118) hydrogen bonds : angle 4.72692 ( 3267) covalent geometry : bond 0.00400 (25390) covalent geometry : angle 0.56856 (34412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 177 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7064 (tm) REVERT: A 469 ASP cc_start: 0.8863 (t70) cc_final: 0.8647 (t0) REVERT: B 69 GLN cc_start: 0.6795 (tp-100) cc_final: 0.6573 (tp40) REVERT: B 246 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7439 (mtt) REVERT: B 476 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: C 131 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: C 231 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8233 (t0) REVERT: C 284 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7675 (ttt180) REVERT: C 334 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: D 87 MET cc_start: 0.8810 (mtp) cc_final: 0.8585 (mtp) REVERT: D 225 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7735 (mtt) REVERT: E 350 ASP cc_start: 0.8889 (t0) cc_final: 0.8541 (t0) REVERT: E 374 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8772 (mm-30) REVERT: F 110 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7606 (ttp80) REVERT: F 203 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: e 118 LEU cc_start: 0.4961 (OUTLIER) cc_final: 0.4216 (pt) REVERT: g 24 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: g 26 MET cc_start: 0.8671 (mmt) cc_final: 0.8281 (mmt) outliers start: 90 outliers final: 42 residues processed: 243 average time/residue: 1.2302 time to fit residues: 349.6383 Evaluate side-chains 221 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 167 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 129 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 100 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 274 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN E 109 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 111 GLN F 370 GLN g 55 HIS ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084281 restraints weight = 52499.796| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.18 r_work: 0.3157 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25390 Z= 0.173 Angle : 0.584 11.781 34412 Z= 0.305 Chirality : 0.045 0.187 3975 Planarity : 0.004 0.050 4484 Dihedral : 6.249 85.317 3683 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.20 % Allowed : 17.96 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3260 helix: 1.38 (0.15), residues: 1290 sheet: 0.58 (0.25), residues: 430 loop : -1.28 (0.15), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 139 HIS 0.006 0.001 HIS g 65 PHE 0.014 0.001 PHE F 138 TYR 0.013 0.001 TYR A 475 ARG 0.012 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 1118) hydrogen bonds : angle 4.76210 ( 3267) covalent geometry : bond 0.00411 (25390) covalent geometry : angle 0.58375 (34412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 178 time to evaluate : 2.628 Fit side-chains revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7044 (tm) REVERT: A 469 ASP cc_start: 0.8874 (t70) cc_final: 0.8669 (t0) REVERT: B 69 GLN cc_start: 0.6782 (tp-100) cc_final: 0.6556 (tp40) REVERT: B 246 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7426 (mtt) REVERT: C 131 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: C 284 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7630 (ttt180) REVERT: C 334 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: D 87 MET cc_start: 0.8839 (mtp) cc_final: 0.8583 (mtp) REVERT: D 159 MET cc_start: 0.8194 (mmm) cc_final: 0.7931 (mmp) REVERT: D 225 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7667 (mtt) REVERT: E 350 ASP cc_start: 0.8898 (t0) cc_final: 0.8580 (t0) REVERT: E 374 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8762 (mm-30) REVERT: F 110 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7470 (ttp80) REVERT: F 203 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8237 (mtp) REVERT: g 24 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: g 26 MET cc_start: 0.8746 (mmt) cc_final: 0.8341 (mmt) REVERT: g 113 VAL cc_start: 0.5661 (OUTLIER) cc_final: 0.5430 (m) outliers start: 84 outliers final: 39 residues processed: 240 average time/residue: 1.2265 time to fit residues: 344.0612 Evaluate side-chains 216 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 162 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 322 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 220 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN C 273 GLN D 209 ASN D 366 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.116639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086095 restraints weight = 52027.853| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.19 r_work: 0.3186 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25390 Z= 0.114 Angle : 0.561 15.097 34412 Z= 0.288 Chirality : 0.043 0.203 3975 Planarity : 0.004 0.051 4484 Dihedral : 6.080 86.638 3683 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.33 % Allowed : 19.15 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3260 helix: 1.37 (0.15), residues: 1306 sheet: 0.74 (0.25), residues: 430 loop : -1.22 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.004 0.001 HIS e 38 PHE 0.014 0.001 PHE F 415 TYR 0.013 0.001 TYR A 475 ARG 0.013 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 1118) hydrogen bonds : angle 4.59136 ( 3267) covalent geometry : bond 0.00257 (25390) covalent geometry : angle 0.56087 (34412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 2.954 Fit side-chains revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7073 (tm) REVERT: A 469 ASP cc_start: 0.8841 (t70) cc_final: 0.8615 (t0) REVERT: B 69 GLN cc_start: 0.6806 (tp-100) cc_final: 0.6576 (tp40) REVERT: B 231 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7900 (m-30) REVERT: B 246 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7422 (mtt) REVERT: C 131 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: C 231 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: C 514 TYR cc_start: 0.5942 (m-80) cc_final: 0.5339 (t80) REVERT: D 87 MET cc_start: 0.8715 (mtp) cc_final: 0.8502 (mtp) REVERT: D 159 MET cc_start: 0.8258 (mmm) cc_final: 0.7987 (mmp) REVERT: D 225 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7638 (mtt) REVERT: E 59 GLU cc_start: 0.8494 (pp20) cc_final: 0.8205 (pp20) REVERT: E 147 PHE cc_start: 0.8300 (m-10) cc_final: 0.7931 (m-10) REVERT: E 302 TYR cc_start: 0.6598 (t80) cc_final: 0.6283 (t80) REVERT: E 350 ASP cc_start: 0.8897 (t0) cc_final: 0.8618 (t0) REVERT: E 374 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8774 (mm-30) REVERT: F 203 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8208 (mtp) REVERT: g 26 MET cc_start: 0.8682 (mmt) cc_final: 0.8278 (mmt) REVERT: g 113 VAL cc_start: 0.5645 (OUTLIER) cc_final: 0.5415 (m) REVERT: g 179 MET cc_start: 0.7855 (pmm) cc_final: 0.7538 (pmm) REVERT: g 231 TYR cc_start: 0.8931 (t80) cc_final: 0.8439 (t80) outliers start: 61 outliers final: 39 residues processed: 224 average time/residue: 1.2508 time to fit residues: 329.3961 Evaluate side-chains 216 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 146 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 293 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN C 273 GLN D 209 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.116388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085874 restraints weight = 52359.270| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.20 r_work: 0.3185 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25390 Z= 0.127 Angle : 0.578 12.877 34412 Z= 0.297 Chirality : 0.043 0.212 3975 Planarity : 0.004 0.058 4484 Dihedral : 6.029 86.469 3683 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.25 % Allowed : 19.37 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3260 helix: 1.36 (0.15), residues: 1308 sheet: 0.77 (0.25), residues: 430 loop : -1.19 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.004 0.001 HIS e 38 PHE 0.012 0.001 PHE g 125 TYR 0.013 0.001 TYR A 475 ARG 0.014 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 1118) hydrogen bonds : angle 4.60510 ( 3267) covalent geometry : bond 0.00292 (25390) covalent geometry : angle 0.57838 (34412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7063 (tm) REVERT: A 469 ASP cc_start: 0.8838 (t70) cc_final: 0.8613 (t0) REVERT: B 69 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6606 (tp40) REVERT: B 231 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: B 246 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7385 (mtt) REVERT: C 131 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: C 231 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: D 159 MET cc_start: 0.8278 (mmm) cc_final: 0.8007 (mmp) REVERT: D 225 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7643 (mtt) REVERT: E 59 GLU cc_start: 0.8480 (pp20) cc_final: 0.8185 (pp20) REVERT: E 302 TYR cc_start: 0.6558 (t80) cc_final: 0.6293 (t80) REVERT: E 350 ASP cc_start: 0.8909 (t0) cc_final: 0.8632 (t0) REVERT: E 374 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8754 (mm-30) REVERT: F 110 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7077 (ttp80) REVERT: F 203 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: g 26 MET cc_start: 0.8654 (mmt) cc_final: 0.8236 (mmt) REVERT: g 113 VAL cc_start: 0.5570 (OUTLIER) cc_final: 0.5333 (m) REVERT: g 179 MET cc_start: 0.7869 (pmm) cc_final: 0.7547 (pmm) REVERT: g 231 TYR cc_start: 0.8931 (t80) cc_final: 0.8441 (t80) outliers start: 59 outliers final: 37 residues processed: 222 average time/residue: 1.2480 time to fit residues: 324.0113 Evaluate side-chains 212 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 467 ASP Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 295 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 297 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 172 optimal weight: 0.0570 chunk 232 optimal weight: 0.0970 overall best weight: 0.9698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN D 209 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN g 58 GLN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.116859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.086441 restraints weight = 51834.802| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.18 r_work: 0.3193 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25390 Z= 0.118 Angle : 0.581 18.519 34412 Z= 0.297 Chirality : 0.043 0.217 3975 Planarity : 0.004 0.060 4484 Dihedral : 5.962 86.933 3683 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.02 % Allowed : 19.79 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3260 helix: 1.42 (0.15), residues: 1296 sheet: 0.84 (0.25), residues: 431 loop : -1.14 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 139 HIS 0.004 0.001 HIS e 38 PHE 0.012 0.001 PHE F 415 TYR 0.014 0.001 TYR A 475 ARG 0.014 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1118) hydrogen bonds : angle 4.55384 ( 3267) covalent geometry : bond 0.00268 (25390) covalent geometry : angle 0.58078 (34412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7144 (tm) REVERT: A 402 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7032 (pmm-80) REVERT: A 469 ASP cc_start: 0.8826 (t70) cc_final: 0.8600 (t0) REVERT: B 69 GLN cc_start: 0.6772 (tp-100) cc_final: 0.6533 (tp40) REVERT: B 231 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: B 246 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7351 (mtt) REVERT: C 131 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: C 231 ASP cc_start: 0.8369 (t0) cc_final: 0.8097 (m-30) REVERT: C 514 TYR cc_start: 0.6173 (m-80) cc_final: 0.5513 (t80) REVERT: D 159 MET cc_start: 0.8275 (mmm) cc_final: 0.7975 (mmp) REVERT: D 225 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7668 (mtt) REVERT: E 59 GLU cc_start: 0.8427 (pp20) cc_final: 0.8130 (pp20) REVERT: E 302 TYR cc_start: 0.6588 (t80) cc_final: 0.6304 (t80) REVERT: E 350 ASP cc_start: 0.8899 (t0) cc_final: 0.8573 (t0) REVERT: E 374 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8762 (mm-30) REVERT: F 110 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7072 (ttp80) REVERT: g 26 MET cc_start: 0.8635 (mmt) cc_final: 0.8206 (mmt) REVERT: g 113 VAL cc_start: 0.5708 (OUTLIER) cc_final: 0.5481 (m) REVERT: g 179 MET cc_start: 0.7861 (pmm) cc_final: 0.7637 (ppp) REVERT: g 231 TYR cc_start: 0.8913 (t80) cc_final: 0.8413 (t80) outliers start: 53 outliers final: 36 residues processed: 219 average time/residue: 1.1767 time to fit residues: 303.9965 Evaluate side-chains 212 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 280 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 110 ARG Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 203 MET Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain e residue 20 VAL Chi-restraints excluded: chain e residue 38 HIS Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 113 VAL Chi-restraints excluded: chain g residue 153 VAL Chi-restraints excluded: chain g residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 52 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 257 optimal weight: 0.1980 chunk 102 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN C 273 GLN D 209 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS F 111 GLN g 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.087032 restraints weight = 51882.483| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.20 r_work: 0.3208 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25390 Z= 0.111 Angle : 0.579 19.224 34412 Z= 0.294 Chirality : 0.043 0.213 3975 Planarity : 0.004 0.061 4484 Dihedral : 5.841 87.533 3683 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.95 % Allowed : 20.21 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3260 helix: 1.42 (0.15), residues: 1307 sheet: 0.81 (0.25), residues: 435 loop : -1.08 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 139 HIS 0.003 0.001 HIS e 38 PHE 0.012 0.001 PHE g 125 TYR 0.014 0.001 TYR A 456 ARG 0.014 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1118) hydrogen bonds : angle 4.49358 ( 3267) covalent geometry : bond 0.00251 (25390) covalent geometry : angle 0.57914 (34412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14860.27 seconds wall clock time: 256 minutes 57.33 seconds (15417.33 seconds total)