Starting phenix.real_space_refine on Fri Sep 19 09:59:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi2_60119/09_2025/8zi2_60119.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi2_60119/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zi2_60119/09_2025/8zi2_60119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi2_60119/09_2025/8zi2_60119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zi2_60119/09_2025/8zi2_60119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi2_60119/09_2025/8zi2_60119.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.80, per 1000 atoms: 0.23 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: 2.54 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.33 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: 5.75 Time building geometry restraints manager: 3.42 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: 4.280 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.420 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (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 ARG 0.014 0.001 ARG C 41 TYR 0.018 0.001 TYR D 205 PHE 0.018 0.001 PHE D 175 TRP 0.007 0.002 TRP g 206 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00612 (25390) covalent geometry : angle 0.86380 (34412) hydrogen bonds : bond 0.20404 ( 1118) hydrogen bonds : angle 7.45643 ( 3267) *********************** 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 : 0.807 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: 0.6859 time to fit residues: 262.7068 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 : 1.010 ------------------------------------------------------------------------------- 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 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 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 = 0.3810 r_free = 0.3810 target = 0.117441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087127 restraints weight = 52194.213| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.19 r_work: 0.3184 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25390 Z= 0.146 Angle : 0.605 14.259 34412 Z= 0.320 Chirality : 0.045 0.163 3975 Planarity : 0.005 0.063 4484 Dihedral : 6.807 85.201 3686 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.78 % Allowed : 14.23 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.15), residues: 3260 helix: 1.28 (0.15), residues: 1285 sheet: 0.42 (0.25), residues: 445 loop : -1.24 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 105 TYR 0.026 0.001 TYR g 169 PHE 0.014 0.001 PHE A 410 TRP 0.006 0.001 TRP g 206 HIS 0.003 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00326 (25390) covalent geometry : angle 0.60451 (34412) hydrogen bonds : bond 0.05059 ( 1118) hydrogen bonds : angle 5.38418 ( 3267) *********************** 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 273 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 200 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7053 (tm) REVERT: A 505 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.7928 (pp) REVERT: B 53 MET cc_start: 0.7999 (mtm) cc_final: 0.7402 (mmt) REVERT: B 246 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7400 (mtt) REVERT: D 87 MET cc_start: 0.8972 (mtp) cc_final: 0.8636 (mtp) REVERT: D 159 MET cc_start: 0.8169 (mmm) cc_final: 0.7931 (mmp) REVERT: D 225 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7744 (mtt) REVERT: E 450 MET cc_start: 0.8600 (mmt) cc_final: 0.8288 (mmt) REVERT: e 124 THR cc_start: 0.8143 (m) cc_final: 0.7908 (p) REVERT: g 170 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9155 (mm) REVERT: g 188 LEU cc_start: 0.8707 (pp) cc_final: 0.8474 (pp) REVERT: g 232 GLN cc_start: 0.9118 (tp40) cc_final: 0.8872 (tm-30) outliers start: 73 outliers final: 26 residues processed: 247 average time/residue: 0.6054 time to fit residues: 173.8496 Evaluate side-chains 198 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER 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 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 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 E 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 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 112 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 143 optimal weight: 0.4980 chunk 287 optimal weight: 8.9990 chunk 282 optimal weight: 40.0000 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN 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 ** 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 = 0.3775 r_free = 0.3775 target = 0.114878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084391 restraints weight = 52566.155| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.20 r_work: 0.3155 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25390 Z= 0.189 Angle : 0.598 12.609 34412 Z= 0.316 Chirality : 0.045 0.181 3975 Planarity : 0.004 0.056 4484 Dihedral : 6.635 84.936 3683 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 15.41 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3260 helix: 1.26 (0.15), residues: 1281 sheet: 0.36 (0.25), residues: 440 loop : -1.32 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 251 TYR 0.013 0.001 TYR A 293 PHE 0.024 0.002 PHE g 125 TRP 0.005 0.001 TRP C 139 HIS 0.006 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00447 (25390) covalent geometry : angle 0.59764 (34412) hydrogen bonds : bond 0.05180 ( 1118) hydrogen bonds : angle 5.12087 ( 3267) *********************** 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 261 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7021 (tm) REVERT: A 402 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7051 (pmm-80) REVERT: A 469 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8616 (t0) REVERT: B 53 MET cc_start: 0.8137 (mtm) cc_final: 0.7486 (mmt) REVERT: B 246 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7398 (mtt) REVERT: B 365 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 51 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7340 (mmm-85) REVERT: D 87 MET cc_start: 0.8927 (mtp) cc_final: 0.8643 (mtp) REVERT: D 159 MET cc_start: 0.8199 (mmm) cc_final: 0.7908 (mmp) REVERT: D 225 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7813 (mtt) REVERT: E 266 MET cc_start: 0.1675 (pmm) cc_final: 0.1465 (pmm) REVERT: E 450 MET cc_start: 0.8657 (mmt) cc_final: 0.8291 (mmt) REVERT: g 24 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: g 26 MET cc_start: 0.8616 (mmt) cc_final: 0.8283 (mmt) REVERT: g 188 LEU cc_start: 0.8753 (pp) cc_final: 0.8512 (pp) REVERT: g 262 ASP cc_start: 0.8667 (t0) cc_final: 0.8401 (t0) outliers start: 77 outliers final: 34 residues processed: 239 average time/residue: 0.6153 time to fit residues: 172.2795 Evaluate side-chains 205 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 402 ARG Chi-restraints excluded: chain A residue 444 ASP 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 B residue 365 ILE 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 231 ASP 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 152 VAL Chi-restraints excluded: chain E residue 218 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 354 VAL Chi-restraints excluded: chain F residue 384 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 17 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN E 8 GLN E 248 ASN E 284 GLN ** E 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 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 = 0.3775 r_free = 0.3775 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084449 restraints weight = 52389.827| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.19 r_work: 0.3157 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25390 Z= 0.168 Angle : 0.571 12.326 34412 Z= 0.300 Chirality : 0.045 0.165 3975 Planarity : 0.004 0.054 4484 Dihedral : 6.514 84.096 3683 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.59 % Allowed : 15.68 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.15), residues: 3260 helix: 1.25 (0.15), residues: 1287 sheet: 0.40 (0.25), residues: 434 loop : -1.36 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 41 TYR 0.016 0.001 TYR A 475 PHE 0.018 0.001 PHE g 125 TRP 0.004 0.001 TRP C 139 HIS 0.005 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00395 (25390) covalent geometry : angle 0.57100 (34412) hydrogen bonds : bond 0.04761 ( 1118) hydrogen bonds : angle 4.94248 ( 3267) *********************** 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 275 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 181 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7040 (tm) REVERT: A 469 ASP cc_start: 0.8825 (t70) cc_final: 0.8614 (t0) REVERT: B 246 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: C 284 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7603 (ttt180) REVERT: C 334 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: D 87 MET cc_start: 0.8839 (mtp) cc_final: 0.8578 (mtp) REVERT: D 225 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7864 (mtt) REVERT: E 350 ASP cc_start: 0.8979 (t0) cc_final: 0.8646 (t0) REVERT: E 450 MET cc_start: 0.8712 (mmt) cc_final: 0.8313 (mmt) REVERT: F 203 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (mtp) REVERT: g 24 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7671 (mtp) REVERT: g 26 MET cc_start: 0.8655 (mmt) cc_final: 0.8285 (mmt) REVERT: g 232 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8875 (tm-30) REVERT: g 262 ASP cc_start: 0.8664 (t0) cc_final: 0.8393 (t0) outliers start: 94 outliers final: 39 residues processed: 250 average time/residue: 0.6062 time to fit residues: 177.9685 Evaluate side-chains 213 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 444 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 65 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 45 LEU Chi-restraints excluded: chain C residue 95 VAL 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 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 E residue 152 VAL 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 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 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 150 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** e 100 ASN ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084906 restraints weight = 52175.631| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.19 r_work: 0.3166 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25390 Z= 0.144 Angle : 0.557 12.294 34412 Z= 0.290 Chirality : 0.044 0.174 3975 Planarity : 0.004 0.050 4484 Dihedral : 6.378 84.875 3683 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.39 % Allowed : 16.51 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.15), residues: 3260 helix: 1.28 (0.15), residues: 1301 sheet: 0.48 (0.25), residues: 442 loop : -1.34 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 41 TYR 0.015 0.001 TYR A 475 PHE 0.017 0.001 PHE F 415 TRP 0.004 0.001 TRP C 139 HIS 0.004 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00335 (25390) covalent geometry : angle 0.55719 (34412) hydrogen bonds : bond 0.04419 ( 1118) hydrogen bonds : angle 4.80816 ( 3267) *********************** 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 272 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 183 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7084 (tm) REVERT: A 398 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7684 (mt) REVERT: A 402 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7057 (pmm-80) REVERT: A 469 ASP cc_start: 0.8851 (t70) cc_final: 0.8629 (t0) REVERT: B 246 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7463 (mtt) REVERT: C 284 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7637 (ttt180) REVERT: C 285 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: C 334 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: D 51 ARG cc_start: 0.7435 (ttm170) cc_final: 0.7187 (mmm-85) REVERT: D 87 MET cc_start: 0.8799 (mtp) cc_final: 0.8559 (mtp) REVERT: D 225 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: E 350 ASP cc_start: 0.8942 (t0) cc_final: 0.8629 (t0) REVERT: E 374 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8756 (mm-30) REVERT: E 450 MET cc_start: 0.8716 (mmt) cc_final: 0.8278 (mmt) REVERT: F 110 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7141 (ttp80) REVERT: F 203 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8302 (mtp) REVERT: e 123 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: g 24 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7588 (mtp) REVERT: g 26 MET cc_start: 0.8651 (mmt) cc_final: 0.8284 (mmt) outliers start: 89 outliers final: 40 residues processed: 247 average time/residue: 0.6346 time to fit residues: 182.6472 Evaluate side-chains 219 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 LEU 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 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 C residue 284 ARG Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 334 GLN 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 384 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 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 32 LEU 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 33 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 198 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN D 209 ASN E 109 HIS E 164 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 410 HIS g 55 HIS ** g 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.081517 restraints weight = 53193.992| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.17 r_work: 0.3105 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 25390 Z= 0.295 Angle : 0.688 11.816 34412 Z= 0.363 Chirality : 0.048 0.189 3975 Planarity : 0.005 0.055 4484 Dihedral : 6.814 82.297 3683 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.70 % Allowed : 17.81 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.14), residues: 3260 helix: 0.99 (0.15), residues: 1294 sheet: 0.10 (0.25), residues: 449 loop : -1.58 (0.15), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 41 TYR 0.017 0.002 TYR g 67 PHE 0.021 0.002 PHE F 138 TRP 0.009 0.002 TRP A 139 HIS 0.010 0.002 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00713 (25390) covalent geometry : angle 0.68824 (34412) hydrogen bonds : bond 0.05904 ( 1118) hydrogen bonds : angle 5.18283 ( 3267) *********************** 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 275 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 178 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6977 (tm) REVERT: A 290 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: A 469 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8685 (t0) REVERT: A 505 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8046 (pp) REVERT: B 246 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7538 (mtt) REVERT: B 476 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: C 41 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7777 (ttm110) REVERT: C 131 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7497 (mt-10) REVERT: C 284 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7549 (ttt180) REVERT: C 285 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: C 334 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: D 225 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7763 (mtt) REVERT: E 350 ASP cc_start: 0.8994 (t0) cc_final: 0.8680 (t0) REVERT: E 374 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8749 (mm-30) REVERT: E 450 MET cc_start: 0.8613 (mmt) cc_final: 0.8291 (mmt) REVERT: F 110 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7591 (ttp80) REVERT: e 123 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: g 24 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7767 (mtp) REVERT: g 26 MET cc_start: 0.8697 (mmt) cc_final: 0.8301 (mmt) REVERT: g 262 ASP cc_start: 0.8683 (t0) cc_final: 0.8430 (t0) outliers start: 97 outliers final: 48 residues processed: 248 average time/residue: 0.6393 time to fit residues: 184.3451 Evaluate side-chains 222 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 ASP Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 505 ILE 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 110 ASP Chi-restraints excluded: chain B residue 130 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 444 ASP 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 190 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 384 MET Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 218 VAL 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 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 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 70 GLU Chi-restraints excluded: chain e residue 123 GLU Chi-restraints excluded: chain g residue 17 THR Chi-restraints excluded: chain g residue 24 MET Chi-restraints excluded: chain g residue 91 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 101 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 229 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 211 optimal weight: 0.5980 chunk 306 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- 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 111 GLN F 214 ASN F 370 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 = 0.3776 r_free = 0.3776 target = 0.114888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084574 restraints weight = 51981.985| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.18 r_work: 0.3161 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25390 Z= 0.131 Angle : 0.574 12.387 34412 Z= 0.298 Chirality : 0.044 0.200 3975 Planarity : 0.004 0.050 4484 Dihedral : 6.461 83.763 3683 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.71 % Allowed : 18.99 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3260 helix: 1.16 (0.15), residues: 1306 sheet: 0.48 (0.25), residues: 421 loop : -1.46 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 41 TYR 0.014 0.001 TYR A 475 PHE 0.016 0.001 PHE D 175 TRP 0.004 0.001 TRP C 139 HIS 0.004 0.001 HIS g 65 Details of bonding type rmsd covalent geometry : bond 0.00301 (25390) covalent geometry : angle 0.57417 (34412) hydrogen bonds : bond 0.04280 ( 1118) hydrogen bonds : angle 4.79310 ( 3267) *********************** 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 252 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7076 (tm) REVERT: A 398 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 402 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7039 (pmm-80) REVERT: A 469 ASP cc_start: 0.8880 (t70) cc_final: 0.8670 (t0) REVERT: B 246 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7487 (mtt) REVERT: C 41 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7689 (ttm110) REVERT: C 131 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: C 284 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7637 (ttt180) REVERT: C 285 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: D 225 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7881 (mtt) REVERT: E 350 ASP cc_start: 0.8961 (t0) cc_final: 0.8667 (t0) REVERT: E 374 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8739 (mm-30) REVERT: E 450 MET cc_start: 0.8618 (mmt) cc_final: 0.8285 (mmt) REVERT: F 66 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6769 (t) REVERT: F 270 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8518 (m) REVERT: e 123 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: g 26 MET cc_start: 0.8599 (mmt) cc_final: 0.8203 (mmt) outliers start: 71 outliers final: 35 residues processed: 231 average time/residue: 0.6037 time to fit residues: 162.6508 Evaluate side-chains 211 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 LEU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 ASP 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 347 ILE Chi-restraints excluded: chain B residue 476 PHE 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 285 GLU 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 384 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 136 CYS 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 32 LEU Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 100 ASN Chi-restraints excluded: chain e residue 123 GLU Chi-restraints excluded: chain g residue 81 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 234 optimal weight: 8.9990 chunk 134 optimal weight: 0.0040 chunk 192 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084908 restraints weight = 52126.668| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.17 r_work: 0.3164 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2537 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= 0.130 Angle : 0.582 12.782 34412 Z= 0.300 Chirality : 0.044 0.199 3975 Planarity : 0.004 0.050 4484 Dihedral : 6.341 84.152 3683 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.75 % Allowed : 19.45 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 3260 helix: 1.25 (0.15), residues: 1305 sheet: 0.58 (0.25), residues: 425 loop : -1.39 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 41 TYR 0.014 0.001 TYR g 225 PHE 0.014 0.001 PHE g 125 TRP 0.004 0.001 TRP A 139 HIS 0.004 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00299 (25390) covalent geometry : angle 0.58235 (34412) hydrogen bonds : bond 0.04203 ( 1118) hydrogen bonds : angle 4.72795 ( 3267) *********************** 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 248 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7089 (tm) REVERT: A 402 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7003 (pmm-80) REVERT: A 469 ASP cc_start: 0.8873 (t70) cc_final: 0.8665 (t0) REVERT: B 246 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7497 (mtt) REVERT: C 29 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: C 131 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: C 284 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7580 (ttt180) REVERT: C 285 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: C 514 TYR cc_start: 0.6223 (m-80) cc_final: 0.5357 (t80) REVERT: D 159 MET cc_start: 0.8228 (mmm) cc_final: 0.7968 (mmp) REVERT: D 225 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7831 (mtt) REVERT: E 302 TYR cc_start: 0.6538 (t80) cc_final: 0.6121 (t80) REVERT: E 350 ASP cc_start: 0.8939 (t0) cc_final: 0.8642 (t0) REVERT: E 374 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8748 (mm-30) REVERT: E 450 MET cc_start: 0.8713 (mmt) cc_final: 0.8329 (mmt) REVERT: F 66 THR cc_start: 0.7105 (OUTLIER) cc_final: 0.6790 (t) REVERT: F 92 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8354 (mtt-85) REVERT: e 123 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: g 26 MET cc_start: 0.8618 (mmt) cc_final: 0.8217 (mmt) REVERT: g 113 VAL cc_start: 0.5678 (OUTLIER) cc_final: 0.5461 (m) outliers start: 72 outliers final: 38 residues processed: 231 average time/residue: 0.6120 time to fit residues: 163.0387 Evaluate side-chains 217 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 167 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 ASP 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 347 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 29 GLU 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 285 GLU 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 384 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 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 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 32 LEU Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 123 GLU Chi-restraints excluded: chain g residue 81 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 208 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 205 optimal weight: 0.5980 chunk 315 optimal weight: 0.9980 chunk 281 optimal weight: 5.9990 chunk 152 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.3782 r_free = 0.3782 target = 0.115262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084973 restraints weight = 52342.012| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.18 r_work: 0.3166 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25390 Z= 0.134 Angle : 0.587 12.863 34412 Z= 0.302 Chirality : 0.044 0.218 3975 Planarity : 0.004 0.050 4484 Dihedral : 6.242 84.463 3683 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 19.98 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.15), residues: 3260 helix: 1.29 (0.15), residues: 1303 sheet: 0.61 (0.25), residues: 426 loop : -1.34 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 41 TYR 0.016 0.001 TYR A 475 PHE 0.014 0.001 PHE g 125 TRP 0.003 0.001 TRP A 139 HIS 0.004 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00312 (25390) covalent geometry : angle 0.58655 (34412) hydrogen bonds : bond 0.04170 ( 1118) hydrogen bonds : angle 4.67994 ( 3267) *********************** 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 238 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7114 (tm) REVERT: A 402 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7020 (pmm-80) REVERT: A 469 ASP cc_start: 0.8868 (t70) cc_final: 0.8660 (t0) REVERT: B 231 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: B 246 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: C 29 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: C 131 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: C 284 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: C 285 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: D 159 MET cc_start: 0.8239 (mmm) cc_final: 0.7953 (mmp) REVERT: D 225 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7755 (mtt) REVERT: E 59 GLU cc_start: 0.8436 (pp20) cc_final: 0.8161 (pp20) REVERT: E 302 TYR cc_start: 0.6611 (t80) cc_final: 0.6163 (t80) REVERT: E 350 ASP cc_start: 0.8951 (t0) cc_final: 0.8633 (t0) REVERT: E 374 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8761 (mm-30) REVERT: E 450 MET cc_start: 0.8697 (mmt) cc_final: 0.8298 (mmt) REVERT: F 66 THR cc_start: 0.7097 (OUTLIER) cc_final: 0.6785 (t) REVERT: F 92 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8366 (mtt-85) REVERT: g 26 MET cc_start: 0.8650 (mmt) cc_final: 0.8231 (mmt) REVERT: g 113 VAL cc_start: 0.5650 (OUTLIER) cc_final: 0.5436 (m) outliers start: 67 outliers final: 38 residues processed: 224 average time/residue: 0.5925 time to fit residues: 154.5821 Evaluate side-chains 218 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 398 LEU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 ASP 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 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 29 GLU 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 285 GLU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 358 THR 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 E residue 218 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 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 218 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 70 GLU Chi-restraints excluded: chain g residue 81 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 311 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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** F 111 GLN F 214 ASN 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 = 0.3734 r_free = 0.3734 target = 0.112001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081807 restraints weight = 52980.919| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.16 r_work: 0.3111 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 25390 Z= 0.286 Angle : 0.705 16.723 34412 Z= 0.369 Chirality : 0.048 0.216 3975 Planarity : 0.005 0.053 4484 Dihedral : 6.667 82.126 3683 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.33 % Allowed : 20.29 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3260 helix: 1.06 (0.15), residues: 1291 sheet: 0.24 (0.25), residues: 440 loop : -1.55 (0.15), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 41 TYR 0.016 0.002 TYR A 475 PHE 0.019 0.002 PHE F 138 TRP 0.010 0.002 TRP A 139 HIS 0.008 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00692 (25390) covalent geometry : angle 0.70503 (34412) hydrogen bonds : bond 0.05639 ( 1118) hydrogen bonds : angle 5.04834 ( 3267) ********************** 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 229 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: A 238 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6896 (tm) REVERT: A 402 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7129 (pmm-80) REVERT: A 469 ASP cc_start: 0.8893 (t70) cc_final: 0.8685 (t0) REVERT: B 246 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7499 (mtt) REVERT: C 29 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: C 131 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: C 284 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7584 (ttt180) REVERT: C 285 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: D 225 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: E 59 GLU cc_start: 0.8406 (pp20) cc_final: 0.8135 (pp20) REVERT: E 302 TYR cc_start: 0.6533 (t80) cc_final: 0.6055 (t80) REVERT: E 350 ASP cc_start: 0.8995 (t0) cc_final: 0.8686 (t0) REVERT: E 374 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8754 (mm-30) REVERT: E 450 MET cc_start: 0.8605 (mmt) cc_final: 0.8250 (mmt) REVERT: g 26 MET cc_start: 0.8654 (mmt) cc_final: 0.8264 (mmt) REVERT: g 113 VAL cc_start: 0.5693 (OUTLIER) cc_final: 0.5488 (m) REVERT: g 262 ASP cc_start: 0.8689 (t0) cc_final: 0.8451 (t0) outliers start: 61 outliers final: 39 residues processed: 216 average time/residue: 0.5826 time to fit residues: 146.3522 Evaluate side-chains 210 residues out of total 2622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU 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 398 LEU Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 ASP 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 331 ILE Chi-restraints excluded: chain B residue 476 PHE Chi-restraints excluded: chain C residue 29 GLU 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 285 GLU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 444 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 218 VAL Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 218 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 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 210 optimal weight: 0.9990 chunk 265 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 273 GLN D 209 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3770 r_free = 0.3770 target = 0.114513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.084222 restraints weight = 52231.799| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.17 r_work: 0.3156 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25390 Z= 0.149 Angle : 0.614 12.891 34412 Z= 0.318 Chirality : 0.044 0.214 3975 Planarity : 0.004 0.057 4484 Dihedral : 6.410 83.694 3683 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.10 % Allowed : 20.82 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.15), residues: 3260 helix: 1.21 (0.15), residues: 1299 sheet: 0.47 (0.25), residues: 431 loop : -1.48 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 41 TYR 0.016 0.001 TYR A 475 PHE 0.013 0.001 PHE g 125 TRP 0.005 0.001 TRP A 139 HIS 0.004 0.001 HIS e 38 Details of bonding type rmsd covalent geometry : bond 0.00350 (25390) covalent geometry : angle 0.61376 (34412) hydrogen bonds : bond 0.04374 ( 1118) hydrogen bonds : angle 4.78834 ( 3267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7221.21 seconds wall clock time: 123 minutes 54.75 seconds (7434.75 seconds total)