Starting phenix.real_space_refine on Fri Jun 27 17:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmp_25998/06_2025/7tmp_25998.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.139 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 2 5.49 5 Mg 1 5.21 5 S 91 5.16 5 C 20533 2.51 5 N 5797 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32105 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4228 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 435 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 30, 'ASN:plan1': 3, 'GLN:plan1': 4, 'ASP:plan': 30} Unresolved non-hydrogen planarities: 242 Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3380 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ASN:plan1': 6, 'ARG:plan': 2, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 4098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4098 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 561} Unresolved non-hydrogen bonds: 476 Unresolved non-hydrogen angles: 587 Unresolved non-hydrogen dihedrals: 376 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 29, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 31, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 307 Chain: "D" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3350 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 308 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 25, 'ASN:plan1': 7, 'ARG:plan': 1, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 189 Chain: "E" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4169 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 559} Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 6, 'ASP:plan': 27, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 248 Chain: "F" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3366 Classifications: {'peptide': 459} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 24, 'ARG:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 17} Unresolved non-hydrogen planarities: 175 Chain: "G" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1237 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "H" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 484 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 94 Chain: "I" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1366 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 5, 'TRANS': 211} Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 457 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 225 Chain: "J" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 588 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 1, 'TRANS': 106} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "K" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1265 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 5, 'TRANS': 190} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 10, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 187 Chain: "L" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 486 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1316 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 259 Chain: "N" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 454 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 196 Chain: "P" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2193 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 410} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1426 Unresolved non-hydrogen angles: 1821 Unresolved non-hydrogen dihedrals: 1158 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 30, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 718 Chain: "A" 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: 20.30, per 1000 atoms: 0.63 Number of scatterers: 32105 At special positions: 0 Unit cell: (134.93, 139.05, 203.94, 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 91 16.00 P 2 15.00 Mg 1 11.99 O 5681 8.00 N 5797 7.00 C 20533 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: 8.77 Conformation dependent library (CDL) restraints added in 4.7 seconds 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8972 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 44 sheets defined 54.5% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 99 through 102 removed outlier: 4.079A pdb=" N GLU A 102 " --> pdb=" O GLY A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 273 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.881A pdb=" N MET A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.956A pdb=" N GLY A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 307 " --> pdb=" O MET A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 307' Processing helix chain 'A' and resid 327 through 346 removed outlier: 4.003A pdb=" N ALA A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 418 through 422 removed outlier: 3.610A pdb=" N GLY A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A 422 " --> pdb=" O ALA A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 418 through 422' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 463 through 474 removed outlier: 4.590A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 584 through 587 Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 616 Processing helix chain 'B' and resid 14 through 20 removed outlier: 4.153A pdb=" N GLN B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.675A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.531A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B 238 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 4.217A pdb=" N ARG B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 395 through 421 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 261 through 272 Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 325 through 346 removed outlier: 4.793A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 394 Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.534A pdb=" N GLY C 421 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP C 422 " --> pdb=" O ALA C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 463 through 475 removed outlier: 4.811A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 502 Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 539 through 564 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 593 through 615 removed outlier: 3.744A pdb=" N THR C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.973A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 162 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.770A pdb=" N ARG D 237 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.596A pdb=" N ARG D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 318 Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.539A pdb=" N ALA D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 421 removed outlier: 4.184A pdb=" N ALA D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.795A pdb=" N SER D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 259 through 273 removed outlier: 4.286A pdb=" N THR E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 removed outlier: 3.601A pdb=" N VAL E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 325 through 346 removed outlier: 4.404A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 425 through 435 Processing helix chain 'E' and resid 442 through 448 Processing helix chain 'E' and resid 463 through 475 removed outlier: 4.417A pdb=" N LYS E 469 " --> pdb=" O ASN E 465 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE E 470 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 564 Processing helix chain 'E' and resid 566 through 574 Processing helix chain 'E' and resid 574 through 584 Processing helix chain 'E' and resid 592 through 611 removed outlier: 3.700A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE E 611 " --> pdb=" O MET E 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.630A pdb=" N GLY F 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 233 Processing helix chain 'F' and resid 250 through 269 removed outlier: 3.965A pdb=" N ILE F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 368 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 420 Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 467 through 468 No H-bonds generated for 'chain 'F' and resid 467 through 468' Processing helix chain 'F' and resid 469 through 473 removed outlier: 3.513A pdb=" N LEU F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'G' and resid 46 through 113 removed outlier: 3.532A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 removed outlier: 3.641A pdb=" N LYS G 118 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Proline residue: G 119 - end of helix removed outlier: 3.541A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 164 removed outlier: 5.527A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'H' and resid 30 through 104 removed outlier: 3.787A pdb=" N ILE H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 114 removed outlier: 4.349A pdb=" N ARG I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 131 removed outlier: 3.697A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 164 removed outlier: 5.587A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 Processing helix chain 'I' and resid 214 through 223 Processing helix chain 'J' and resid 6 through 63 Processing helix chain 'J' and resid 64 through 104 removed outlier: 3.735A pdb=" N ALA J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 113 removed outlier: 3.585A pdb=" N ALA K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 145 through 152 Processing helix chain 'K' and resid 152 through 164 Processing helix chain 'K' and resid 202 through 214 Processing helix chain 'K' and resid 214 through 222 Processing helix chain 'L' and resid 26 through 68 removed outlier: 3.580A pdb=" N LEU L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 104 removed outlier: 4.281A pdb=" N GLU L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 76 Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 128 through 176 Processing helix chain 'M' and resid 176 through 217 Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 70 through 77 removed outlier: 3.749A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 Processing helix chain 'N' and resid 106 through 111 removed outlier: 3.687A pdb=" N ARG N 111 " --> pdb=" O SER N 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 23 removed outlier: 3.742A pdb=" N ARG P 23 " --> pdb=" O ILE P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 33 Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 76 through 87 Processing helix chain 'P' and resid 89 through 106 Processing helix chain 'P' and resid 110 through 120 Processing helix chain 'P' and resid 120 through 131 Processing helix chain 'P' and resid 135 through 152 removed outlier: 4.107A pdb=" N GLN P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 167 Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 179 through 194 Processing helix chain 'P' and resid 196 through 210 Processing helix chain 'P' and resid 210 through 223 removed outlier: 3.789A pdb=" N LEU P 214 " --> pdb=" O PHE P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 256 removed outlier: 4.209A pdb=" N ASN P 256 " --> pdb=" O LEU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 removed outlier: 3.567A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR P 267 " --> pdb=" O LEU P 263 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 281 Processing helix chain 'P' and resid 283 through 299 Processing helix chain 'P' and resid 304 through 316 Processing helix chain 'P' and resid 317 through 328 Processing helix chain 'P' and resid 332 through 353 removed outlier: 3.767A pdb=" N GLU P 352 " --> pdb=" O ASN P 348 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 366 Processing helix chain 'P' and resid 371 through 376 removed outlier: 3.505A pdb=" N VAL P 375 " --> pdb=" O SER P 371 " (cutoff:3.500A) Processing helix chain 'P' and resid 376 through 408 removed outlier: 5.044A pdb=" N ASP P 385 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU P 386 " --> pdb=" O ASP P 382 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 411 No H-bonds generated for 'chain 'P' and resid 409 through 411' Processing helix chain 'P' and resid 413 through 433 Processing helix chain 'P' and resid 435 through 444 removed outlier: 4.152A pdb=" N ASP P 439 " --> pdb=" O PRO P 435 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 454 Processing helix chain 'P' and resid 458 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 91 removed outlier: 7.786A pdb=" N THR A 88 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N LYS A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS A 90 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 70 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.542A pdb=" N ALA A 277 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.542A pdb=" N ALA A 277 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 279 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 173 removed outlier: 3.887A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 152 removed outlier: 5.760A pdb=" N ILE A 182 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU A 201 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA9, first strand: chain 'I' and resid 171 through 174 removed outlier: 4.181A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 26 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL B 31 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 59 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU C 38 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE C 27 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 25 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU C 48 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU C 47 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB2, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AB3, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.169A pdb=" N ARG B 321 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.698A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AB6, first strand: chain 'C' and resid 93 through 96 Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.364A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.364A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 414 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 173 removed outlier: 3.905A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP C 139 " --> pdb=" O TYR C 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.526A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 207 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 377 removed outlier: 6.196A pdb=" N PHE C 380 " --> pdb=" O ALA C 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 171 through 174 removed outlier: 6.845A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.668A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 112 through 113 removed outlier: 6.366A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN D 243 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA D 214 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 279 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.220A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC8, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.182A pdb=" N ILE D 172 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE D 359 " --> pdb=" O PRO D 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AD1, first strand: chain 'E' and resid 104 through 105 removed outlier: 5.769A pdb=" N TYR E 105 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR E 321 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL E 318 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR E 280 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASN E 320 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY E 282 " --> pdb=" O ASN E 320 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP E 355 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 281 " --> pdb=" O ASP E 355 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 104 through 105 removed outlier: 5.769A pdb=" N TYR E 105 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N THR E 321 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL E 318 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR E 280 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASN E 320 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY E 282 " --> pdb=" O ASN E 320 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA E 277 " --> pdb=" O SER E 351 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE E 353 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ASP E 355 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 281 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG E 406 " --> pdb=" O ALA E 400 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 152 removed outlier: 3.752A pdb=" N TRP E 184 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 232 through 233 removed outlier: 4.629A pdb=" N CYS E 246 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD7, first strand: chain 'E' and resid 375 through 377 removed outlier: 6.218A pdb=" N PHE E 380 " --> pdb=" O ALA E 376 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 437 through 438 Processing sheet with id=AD9, first strand: chain 'F' and resid 32 through 35 removed outlier: 4.604A pdb=" N VAL F 34 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA G 137 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 101 through 104 Processing sheet with id=AE2, first strand: chain 'F' and resid 111 through 113 removed outlier: 3.658A pdb=" N ARG F 111 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ASN F 243 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ALA F 214 " --> pdb=" O ASN F 243 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.243A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.590A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 334 through 337 removed outlier: 5.871A pdb=" N ILE F 172 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N MET F 337 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER F 174 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE F 173 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE F 359 " --> pdb=" O PRO F 377 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 92 through 98 Processing sheet with id=AE7, first strand: chain 'N' and resid 8 through 10 removed outlier: 6.611A pdb=" N ALA N 9 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 28 through 29 2239 hydrogen bonds defined for protein. 6522 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: 14.97 Time building geometry restraints manager: 10.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5233 1.30 - 1.43: 7900 1.43 - 1.56: 19340 1.56 - 1.68: 3 1.68 - 1.81: 165 Bond restraints: 32641 Sorted by residual: bond pdb=" C ARG G 206 " pdb=" O ARG G 206 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.26e-02 6.30e+03 2.34e+01 bond pdb=" C ASP F 159 " pdb=" O ASP F 159 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" CA GLY I 187 " pdb=" C GLY I 187 " ideal model delta sigma weight residual 1.516 1.461 0.055 1.37e-02 5.33e+03 1.62e+01 bond pdb=" C LEU C 48 " pdb=" O LEU C 48 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.21e-02 6.83e+03 1.52e+01 bond pdb=" C VAL H 102 " pdb=" O VAL H 102 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.17e-02 7.31e+03 1.49e+01 ... (remaining 32636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 43979 1.76 - 3.53: 595 3.53 - 5.29: 106 5.29 - 7.05: 17 7.05 - 8.82: 4 Bond angle restraints: 44701 Sorted by residual: angle pdb=" N THR F 160 " pdb=" CA THR F 160 " pdb=" C THR F 160 " ideal model delta sigma weight residual 111.28 118.15 -6.87 1.09e+00 8.42e-01 3.97e+01 angle pdb=" N VAL H 102 " pdb=" CA VAL H 102 " pdb=" C VAL H 102 " ideal model delta sigma weight residual 110.62 106.18 4.44 1.02e+00 9.61e-01 1.89e+01 angle pdb=" N GLY A 89 " pdb=" CA GLY A 89 " pdb=" C GLY A 89 " ideal model delta sigma weight residual 115.32 109.62 5.70 1.38e+00 5.25e-01 1.70e+01 angle pdb=" N THR H 101 " pdb=" CA THR H 101 " pdb=" C THR H 101 " ideal model delta sigma weight residual 111.69 116.42 -4.73 1.23e+00 6.61e-01 1.48e+01 angle pdb=" N ARG C 359 " pdb=" CA ARG C 359 " pdb=" C ARG C 359 " ideal model delta sigma weight residual 111.28 107.43 3.85 1.09e+00 8.42e-01 1.25e+01 ... (remaining 44696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18128 17.98 - 35.96: 1043 35.96 - 53.94: 188 53.94 - 71.91: 23 71.91 - 89.89: 16 Dihedral angle restraints: 19398 sinusoidal: 5499 harmonic: 13899 Sorted by residual: dihedral pdb=" CA LYS B 384 " pdb=" C LYS B 384 " pdb=" N SER B 385 " pdb=" CA SER B 385 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU C 100 " pdb=" C LEU C 100 " pdb=" N MET C 101 " pdb=" CA MET C 101 " ideal model delta harmonic sigma weight residual 180.00 -157.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ALA B 386 " pdb=" C ALA B 386 " pdb=" N ILE B 387 " pdb=" CA ILE B 387 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 19395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4800 0.061 - 0.122: 674 0.122 - 0.183: 37 0.183 - 0.244: 4 0.244 - 0.306: 2 Chirality restraints: 5517 Sorted by residual: chirality pdb=" CA MET F 161 " pdb=" N MET F 161 " pdb=" C MET F 161 " pdb=" CB MET F 161 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA THR F 160 " pdb=" N THR F 160 " pdb=" C THR F 160 " pdb=" CB THR F 160 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA THR C 88 " pdb=" N THR C 88 " pdb=" C THR C 88 " pdb=" CB THR C 88 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 5514 not shown) Planarity restraints: 5807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 477 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.48e+00 pdb=" N PRO D 478 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 478 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 478 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 184 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL I 184 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL I 184 " 0.016 2.00e-02 2.50e+03 pdb=" N SER I 185 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 100 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU H 100 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU H 100 " -0.015 2.00e-02 2.50e+03 pdb=" N THR H 101 " -0.014 2.00e-02 2.50e+03 ... (remaining 5804 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 191 2.57 - 3.15: 26710 3.15 - 3.74: 53373 3.74 - 4.32: 68275 4.32 - 4.90: 118892 Nonbonded interactions: 267441 Sorted by model distance: nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 702 " model vdw 1.989 2.170 nonbonded pdb=" OG1 THR A 263 " pdb="MG MG A 702 " model vdw 2.019 2.170 nonbonded pdb=" O TYR B 468 " pdb=" OH TYR B 485 " model vdw 2.198 3.040 nonbonded pdb=" O TYR F 468 " pdb=" OH TYR F 485 " model vdw 2.212 3.040 nonbonded pdb=" NZ LYS B 169 " pdb=" OE2 GLU B 355 " model vdw 2.231 3.120 ... (remaining 267436 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 24 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 54 or (resid 55 and (name N or nam \ e CA or name C or name O or name CB )) or resid 56 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 112 or ( \ resid 113 through 114 and (name N or name CA or name C or name O or name CB )) o \ r resid 115 through 116 or (resid 117 through 121 and (name N or name CA or name \ C or name O or name CB )) or resid 122 through 125 or (resid 126 and (name N or \ name CA or name C or name O or name CB )) or resid 127 through 129 or (resid 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or re \ sid 149 through 177 or (resid 178 and (name N or name CA or name C or name O or \ name CB )) or resid 179 through 180 or (resid 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 or (resid 183 and (name N or name CA or \ name C or name O or name CB )) or resid 184 through 189 or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or resid 191 through 194 or (resi \ d 195 and (name N or name CA or name C or name O or name CB )) or resid 196 thro \ ugh 205 or (resid 206 through 208 and (name N or name CA or name C or name O or \ name CB )) or resid 209 through 234 or (resid 235 and (name N or name CA or name \ C or name O or name CB )) or resid 236 through 240 or (resid 241 through 242 an \ d (name N or name CA or name C or name O or name CB )) or resid 243 through 257 \ or (resid 258 and (name N or name CA or name C or name O or name CB )) or resid \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 or (resid 262 through 266 and (name N or name CA or name C or name O or \ name CB )) or resid 267 through 268 or (resid 269 through 271 and (name N or nam \ e CA or name C or name O or name CB )) or resid 272 or (resid 273 through 277 an \ d (name N or name CA or name C or name O or name CB )) or resid 278 through 288 \ or (resid 289 and (name N or name CA or name C or name O or name CB )) or resid \ 290 through 294 or (resid 295 through 296 and (name N or name CA or name C or na \ me O or name CB )) or resid 297 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 314 or (resid 315 and (n \ ame N or name CA or name C or name O or name CB )) or resid 316 through 329 or ( \ resid 330 through 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333 through 372 or (resid 373 and (name N or name CA or name C or name O \ or name CB )) or resid 374 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 406 or (resi \ d 407 and (name N or name CA or name C or name O or name CB )) or resid 408 or ( \ resid 409 and (name N or name CA or name C or name O or name CB )) or resid 410 \ through 416 or (resid 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 through 422 or (resid 423 through 425 and (name N or name CA or \ name C or name O or name CB )) or resid 426 through 442 or (resid 443 through 44 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 445 through \ 446 or (resid 447 through 451 and (name N or name CA or name C or name O or name \ CB )) or resid 452 or (resid 453 and (name N or name CA or name C or name O or \ name CB )) or resid 454 or (resid 455 through 459 and (name N or name CA or name \ C or name O or name CB )) or resid 460 or (resid 461 and (name N or name CA or \ name C or name O or name CB )) or resid 462 through 464 or (resid 465 and (name \ N or name CA or name C or name O or name CB )) or resid 466 through 473 or (resi \ d 474 and (name N or name CA or name C or name O or name CB )) or resid 475 thro \ ugh 482 or (resid 483 and (name N or name CA or name C or name O or name CB )) o \ r resid 484 through 490 or (resid 491 through 502 and (name N or name CA or name \ C or name O or name CB )) or resid 503 through 509 or (resid 510 through 512 an \ d (name N or name CA or name C or name O or name CB )) or resid 513 through 528 \ or (resid 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 or (resid 531 through 533 and (name N or name CA or name C or name O or name \ CB )) or resid 534 through 537 or (resid 538 and (name N or name CA or name C o \ r name O or name CB )) or resid 539 through 544 or (resid 545 and (name N or nam \ e CA or name C or name O or name CB )) or resid 546 or (resid 547 and (name N or \ name CA or name C or name O or name CB )) or resid 548 through 557 or (resid 55 \ 8 through 563 and (name N or name CA or name C or name O or name CB )) or resid \ 564 through 569 or (resid 570 through 574 and (name N or name CA or name C or na \ me O or name CB )) or resid 575 through 578 or (resid 579 through 580 and (name \ N or name CA or name C or name O or name CB )) or resid 581 or (resid 582 throug \ h 584 and (name N or name CA or name C or name O or name CB )) or resid 585 thro \ ugh 587 or (resid 588 and (name N or name CA or name C or name O or name CB )) o \ r resid 589 or (resid 590 through 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 through 602 or (resid 603 and (name N or name CA or \ name C or name O or name CB )) or resid 604 through 606 or (resid 607 through 61 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 35 or (resid 36 through 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 or (resid 41 and (name N or name CA or na \ me C or name O or name CB )) or resid 42 or (resid 43 through 44 and (name N or \ name CA or name C or name O or name CB )) or resid 45 through 50 or (resid 51 an \ d (name N or name CA or name C or name O or name CB )) or resid 52 through 58 or \ (resid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 \ through 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) \ or resid 84 through 92 or (resid 93 and (name N or name CA or name C or name O \ or name CB )) or resid 94 through 107 or (resid 108 and (name N or name CA or na \ me C or name O or name CB )) or resid 109 through 118 or (resid 119 through 121 \ and (name N or name CA or name C or name O or name CB )) or resid 122 through 12 \ 5 or (resid 126 and (name N or name CA or name C or name O or name CB )) or resi \ d 127 through 129 or (resid 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 139 or (resid 140 and (name N or name CA or name C \ or name O or name CB )) or resid 141 through 147 or (resid 148 and (name N or n \ ame CA or name C or name O or name CB )) or resid 149 through 159 or (resid 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 16 \ 2 or (resid 163 and (name N or name CA or name C or name O or name CB )) or resi \ d 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) or \ resid 166 through 167 or (resid 168 through 169 and (name N or name CA or name C \ or name O or name CB )) or resid 170 through 177 or (resid 178 and (name N or n \ ame CA or name C or name O or name CB )) or resid 179 through 180 or (resid 181 \ and (name N or name CA or name C or name O or name CB )) or resid 182 or (resid \ 183 and (name N or name CA or name C or name O or name CB )) or resid 184 throug \ h 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) or \ resid 191 through 234 or (resid 235 and (name N or name CA or name C or name O o \ r name CB )) or resid 236 through 240 or (resid 241 through 242 and (name N or n \ ame CA or name C or name O or name CB )) or resid 243 through 250 or (resid 251 \ and (name N or name CA or name C or name O or name CB )) or resid 252 through 25 \ 7 or (resid 258 and (name N or name CA or name C or name O or name CB )) or (res \ id 259 through 266 and (name N or name CA or name C or name O or name CB )) or r \ esid 267 or (resid 268 through 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 273 or (resid 274 through 277 and (name N or na \ me CA or name C or name O or name CB )) or resid 278 through 291 or (resid 292 a \ nd (name N or name CA or name C or name O or name CB )) or resid 293 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 through 392 or (resid 393 and (name N or name CA or name C or name O or nam \ e CB )) or resid 394 through 408 or (resid 409 and (name N or name CA or name C \ or name O or name CB )) or resid 410 or (resid 411 and (name N or name CA or nam \ e C or name O or name CB )) or resid 412 through 415 or (resid 416 through 417 a \ nd (name N or name CA or name C or name O or name CB )) or resid 418 through 422 \ or (resid 423 through 425 and (name N or name CA or name C or name O or name CB \ )) or resid 426 through 452 or (resid 453 and (name N or name CA or name C or n \ ame O or name CB )) or resid 454 through 457 or (resid 458 through 459 and (name \ N or name CA or name C or name O or name CB )) or resid 460 through 489 or (res \ id 490 through 502 and (name N or name CA or name C or name O or name CB )) or r \ esid 503 through 537 or (resid 538 and (name N or name CA or name C or name O or \ name CB )) or resid 539 through 544 or (resid 545 and (name N or name CA or nam \ e C or name O or name CB )) or resid 546 through 613)) selection = (chain 'E' and ((resid 24 and (name N or name CA or name C or name O or name CB \ )) or resid 25 through 28 or (resid 29 and (name N or name CA or name C or name \ O or name CB )) or resid 30 or (resid 31 and (name N or name CA or name C or nam \ e O or name CB )) or resid 32 through 35 or (resid 36 through 39 and (name N or \ name CA or name C or name O or name CB )) or resid 40 or (resid 41 and (name N o \ r name CA or name C or name O or name CB )) or resid 42 or (resid 43 through 44 \ and (name N or name CA or name C or name O or name CB )) or resid 45 through 50 \ or (resid 51 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 2 through 53 or (resid 54 through 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 65 or (resid 66 and (name N or name CA or name \ C or name O or name CB )) or resid 67 through 82 or (resid 83 and (name N or na \ me CA or name C or name O or name CB )) or resid 84 through 92 or (resid 93 and \ (name N or name CA or name C or name O or name CB )) or resid 94 through 107 or \ (resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 112 or (resid 113 through 114 and (name N or name CA or name C or name \ O or name CB )) or resid 115 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB )) or resid 135 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 162 or (res \ id 163 and (name N or name CA or name C or name O or name CB )) or resid 164 thr \ ough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 205 or (resid 206 through 208 and (name N or name CA or nam \ e C or name O or name CB )) or resid 209 through 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 through 275 or (resid 2 \ 76 through 277 and (name N or name CA or name C or name O or name CB )) or resid \ 278 through 284 or (resid 285 and (name N or name CA or name C or name O or nam \ e CB )) or resid 286 through 288 or (resid 289 and (name N or name CA or name C \ or name O or name CB )) or resid 290 through 301 or (resid 302 through 305 and ( \ name N or name CA or name C or name O or name CB )) or resid 306 through 310 or \ (resid 311 and (name N or name CA or name C or name O or name CB )) or resid 312 \ through 314 or (resid 315 and (name N or name CA or name C or name O or name CB \ )) or resid 316 through 331 or (resid 332 and (name N or name CA or name C or n \ ame O or name CB )) or resid 333 through 356 or (resid 357 and (name N or name C \ A or name C or name O or name CB )) or resid 358 through 365 or (resid 366 and ( \ name N or name CA or name C or name O or name CB )) or resid 367 or (resid 368 a \ nd (name N or name CA or name C or name O or name CB )) or resid 369 through 372 \ or (resid 373 and (name N or name CA or name C or name O or name CB )) or resid \ 374 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB )) or resid 408 through 415 or (resid 416 through 417 and ( \ name N or name CA or name C or name O or name CB )) or resid 418 through 423 or \ (resid 424 through 425 and (name N or name CA or name C or name O or name CB )) \ or resid 426 through 446 or (resid 447 through 451 and (name N or name CA or nam \ e C or name O or name CB )) or resid 452 through 454 or (resid 455 through 459 a \ nd (name N or name CA or name C or name O or name CB )) or resid 460 through 486 \ or (resid 487 and (name N or name CA or name C or name O or name CB )) or resid \ 488 through 489 or (resid 490 through 502 and (name N or name CA or name C or n \ ame O or name CB )) or resid 503 through 509 or (resid 510 through 512 and (name \ N or name CA or name C or name O or name CB )) or resid 513 through 530 or (res \ id 531 through 533 and (name N or name CA or name C or name O or name CB )) or r \ esid 534 through 546 or (resid 547 and (name N or name CA or name C or name O or \ name CB )) or resid 548 through 551 or (resid 552 and (name N or name CA or nam \ e C or name O or name CB )) or resid 553 through 557 or (resid 558 through 563 a \ nd (name N or name CA or name C or name O or name CB )) or resid 564 through 569 \ or (resid 570 through 574 and (name N or name CA or name C or name O or name CB \ )) or (resid 575 through 577 and (name N or name CA or name C or name O or name \ CB )) or resid 578 or (resid 579 through 580 and (name N or name CA or name C o \ r name O or name CB )) or resid 581 through 583 or (resid 584 and (name N or nam \ e CA or name C or name O or name CB )) or resid 585 through 589 or (resid 590 th \ rough 591 and (name N or name CA or name C or name O or name CB )) or resid 592 \ through 602 or (resid 603 and (name N or name CA or name C or name O or name CB \ )) or resid 604 through 605 or (resid 606 through 613 and (name N or name CA or \ name C or name O or name CB )))) } ncs_group { reference = (chain 'B' and (resid 15 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 60 or (resid 61 and (name N or nam \ e CA or name C or name O or name CB )) or resid 62 through 88 or (resid 89 throu \ gh 90 and (name N or name CA or name C or name O or name CB )) or resid 91 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 104 or (resid 105 through 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 136 or (resid 137 and (name N or na \ me CA or name C or name O or name CB )) or resid 138 through 161 or (resid 162 a \ nd (name N or name CA or name C or name O or name CB )) or resid 163 through 173 \ or (resid 174 through 176 and (name N or name CA or name C or name O or name CB \ )) or resid 177 through 194 or (resid 207 and (name N or name CA or name C or n \ ame O or name CB )) or resid 208 or (resid 209 and (name N or name CA or name C \ or name O or name CB )) or resid 210 through 220 or (resid 221 through 222 and ( \ name N or name CA or name C or name O or name CB )) or resid 223 through 226 or \ (resid 227 and (name N or name CA or name C or name O or name CB )) or resid 228 \ through 230 or (resid 231 through 232 and (name N or name CA or name C or name \ O or name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or n \ ame O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name C \ A or name C or name O or name CB )) or resid 240 through 250 or (resid 251 and ( \ name N or name CA or name C or name O or name CB )) or resid 252 through 270 or \ (resid 271 and (name N or name CA or name C or name O or name CB )) or resid 272 \ through 296 or (resid 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 through 300 or (resid 301 and (name N or name CA or name C or n \ ame O or name CB )) or resid 302 through 312 or (resid 313 and (name N or name C \ A or name C or name O or name CB )) or resid 314 through 316 or (resid 317 and ( \ name N or name CA or name C or name O or name CB )) or resid 318 through 325 or \ (resid 326 and (name N or name CA or name C or name O or name CB )) or resid 327 \ through 377 or (resid 378 and (name N or name CA or name C or name O or name CB \ )) or resid 379 or (resid 380 and (name N or name CA or name C or name O or nam \ e CB )) or resid 381 through 383 or (resid 384 through 387 and (name N or name C \ A or name C or name O or name CB )) or (resid 388 through 392 and (name N or nam \ e CA or name C or name O or name CB )) or resid 393 through 399 or (resid 400 th \ rough 401 and (name N or name CA or name C or name O or name CB )) or resid 402 \ through 416 or (resid 417 through 420 and (name N or name CA or name C or name O \ or name CB )) or (resid 421 through 430 and (name N or name CA or name C or nam \ e O or name CB )) or resid 431 through 437 or (resid 438 and (name N or name CA \ or name C or name O or name CB )) or resid 439 through 455 or (resid 456 and (na \ me N or name CA or name C or name O or name CB )) or resid 457 through 469 or (r \ esid 470 through 471 and (name N or name CA or name C or name O or name CB )) or \ resid 472 through 473 or (resid 474 and (name N or name CA or name C or name O \ or name CB )) or resid 475 through 476 or (resid 477 and (name N or name CA or n \ ame C or name O or name CB )) or resid 478 through 485)) selection = (chain 'D' and (resid 15 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB )) or resid 36 through 39 or (resid 40 and ( \ name N or name CA or name C or name O or name CB )) or resid 41 through 50 or (r \ esid 51 through 52 and (name N or name CA or name C or name O or name CB )) or r \ esid 53 through 70 or (resid 71 and (name N or name CA or name C or name O or na \ me CB )) or resid 72 through 83 or (resid 84 and (name N or name CA or name C or \ name O or name CB )) or resid 85 through 124 or (resid 125 and (name N or name \ CA or name C or name O or name CB )) or resid 126 through 132 or (resid 133 and \ (name N or name CA or name C or name O or name CB )) or resid 134 through 136 or \ (resid 137 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 8 through 151 or (resid 152 and (name N or name CA or name C or name O or name C \ B )) or resid 153 through 155 or (resid 156 through 157 and (name N or name CA o \ r name C or name O or name CB )) or resid 158 through 169 or (resid 170 and (nam \ e N or name CA or name C or name O or name CB )) or resid 171 through 220 or (re \ sid 221 through 222 and (name N or name CA or name C or name O or name CB )) or \ resid 223 through 229 or (resid 230 through 232 and (name N or name CA or name C \ or name O or name CB )) or resid 233 through 235 or (resid 236 and (name N or n \ ame CA or name C or name O or name CB )) or resid 237 through 245 or (resid 246 \ through 247 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 8 through 263 or (resid 264 and (name N or name CA or name C or name O or name C \ B )) or resid 265 through 316 or (resid 317 and (name N or name CA or name C or \ name O or name CB )) or resid 318 through 339 or (resid 340 through 341 and (nam \ e N or name CA or name C or name O or name CB )) or resid 342 or (resid 343 and \ (name N or name CA or name C or name O or name CB )) or resid 344 through 384 or \ (resid 385 through 387 and (name N or name CA or name C or name O or name CB )) \ or (resid 388 through 392 and (name N or name CA or name C or name O or name CB \ )) or resid 393 through 397 or (resid 398 and (name N or name CA or name C or n \ ame O or name CB )) or resid 399 through 415 or (resid 416 through 420 and (name \ N or name CA or name C or name O or name CB )) or (resid 421 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 437 or ( \ resid 438 and (name N or name CA or name C or name O or name CB )) or resid 439 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 473 or (resid 474 and (name N or name CA or name C or na \ me O or name CB )) or resid 475 through 482 or (resid 483 and (name N or name CA \ or name C or name O or name CB )) or resid 484 through 485)) selection = (chain 'F' and ((resid 15 through 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 31 or (resid 32 and (name N or na \ me CA or name C or name O or name CB )) or resid 33 through 34 or (resid 35 and \ (name N or name CA or name C or name O or name CB )) or resid 36 through 39 or ( \ resid 40 and (name N or name CA or name C or name O or name CB )) or resid 41 th \ rough 50 or (resid 51 through 52 and (name N or name CA or name C or name O or n \ ame CB )) or resid 53 through 60 or (resid 61 and (name N or name CA or name C o \ r name O or name CB )) or resid 62 through 88 or (resid 89 through 90 and (name \ N or name CA or name C or name O or name CB )) or resid 91 through 98 or (resid \ 99 and (name N or name CA or name C or name O or name CB )) or resid 100 through \ 104 or (resid 105 through 107 and (name N or name CA or name C or name O or nam \ e CB )) or resid 108 through 120 or (resid 121 through 122 and (name N or name C \ A or name C or name O or name CB )) or resid 123 through 151 or (resid 152 and ( \ name N or name CA or name C or name O or name CB )) or resid 153 through 155 or \ (resid 156 through 157 and (name N or name CA or name C or name O or name CB )) \ or resid 158 through 169 or (resid 170 and (name N or name CA or name C or name \ O or name CB )) or resid 171 through 208 or (resid 209 and (name N or name CA or \ name C or name O or name CB )) or resid 210 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 226 or (res \ id 227 and (name N or name CA or name C or name O or name CB )) or resid 228 thr \ ough 229 or (resid 230 through 232 and (name N or name CA or name C or name O or \ name CB )) or resid 233 or (resid 234 and (name N or name CA or name C or name \ O or name CB )) or resid 235 through 238 or (resid 239 and (name N or name CA or \ name C or name O or name CB )) or resid 240 through 245 or (resid 246 through 2 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 248 through \ 263 or (resid 264 and (name N or name CA or name C or name O or name CB )) or r \ esid 265 through 270 or (resid 271 and (name N or name CA or name C or name O or \ name CB )) or resid 272 through 282 or (resid 283 and (name N or name CA or nam \ e C or name O or name CB )) or resid 284 through 285 or (resid 286 through 287 a \ nd (name N or name CA or name C or name O or name CB )) or resid 288 through 289 \ or (resid 290 and (name N or name CA or name C or name O or name CB )) or resid \ 291 through 295 or (resid 296 through 297 and (name N or name CA or name C or n \ ame O or name CB )) or resid 298 through 300 or (resid 301 and (name N or name C \ A or name C or name O or name CB )) or resid 302 through 312 or (resid 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 325 or \ (resid 326 and (name N or name CA or name C or name O or name CB )) or resid 327 \ or (resid 328 and (name N or name CA or name C or name O or name CB )) or resid \ 329 through 338 or (resid 339 through 341 and (name N or name CA or name C or n \ ame O or name CB )) or resid 342 or (resid 343 and (name N or name CA or name C \ or name O or name CB )) or resid 344 through 347 or (resid 348 and (name N or na \ me CA or name C or name O or name CB )) or resid 349 through 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 through 384 \ or (resid 385 through 387 and (name N or name CA or name C or name O or name CB \ )) or (resid 388 through 392 and (name N or name CA or name C or name O or name \ CB )) or resid 393 through 397 or (resid 398 and (name N or name CA or name C o \ r name O or name CB )) or resid 399 or (resid 400 through 401 and (name N or nam \ e CA or name C or name O or name CB )) or resid 402 through 440 or (resid 441 an \ d (name N or name CA or name C or name O or name CB )) or resid 442 through 462 \ or (resid 463 and (name N or name CA or name C or name O or name CB )) or resid \ 464 through 469 or (resid 470 through 471 and (name N or name CA or name C or na \ me O or name CB )) or resid 472 through 485)) } ncs_group { reference = (chain 'G' and ((resid 45 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 89 or (resid 90 through 91 and (name N or name \ CA or name C or name O or name CB )) or resid 92 through 93 or (resid 94 throug \ h 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 101 or (resid 102 through 106 and (name N or name CA or name C or name O or na \ me CB )) or resid 107 through 109 or (resid 110 through 116 and (name N or name \ CA or name C or name O or name CB )) or resid 117 through 122 or (resid 123 and \ (name N or name CA or name C or name O or name CB )) or resid 124 through 145 or \ (resid 146 through 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 157 or (resid 158 and (name N or name CA or name C or name \ O or name CB )) or resid 159 through 164 or (resid 165 through 167 and (name N \ or name CA or name C or name O or name CB )) or resid 168 through 174 or (resid \ 175 through 177 and (name N or name CA or name C or name O or name CB )) or resi \ d 178 through 183 or (resid 184 through 185 and (name N or name CA or name C or \ name O or name CB )) or resid 186 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 231)) selection = (chain 'I' and (resid 45 through 92 or (resid 93 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 101 or (resid 102 throu \ gh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 thr \ ough 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) \ or resid 119 through 122 or (resid 123 and (name N or name CA or name C or name \ O or name CB )) or resid 124 through 126 or (resid 127 through 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 133 or (resid 1 \ 34 and (name N or name CA or name C or name O or name CB )) or resid 135 through \ 183 or (resid 184 through 185 and (name N or name CA or name C or name O or nam \ e CB )) or resid 186 through 197 or (resid 198 and (name N or name CA or name C \ or name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 210 or (resid 2 \ 11 through 214 and (name N or name CA or name C or name O or name CB )) or resid \ 215 through 226 or (resid 227 through 228 and (name N or name CA or name C or n \ ame O or name CB )) or resid 229 through 231)) selection = (chain 'K' and ((resid 45 through 84 and (name N or name CA or name C or name O \ or name CB )) or resid 85 through 92 or (resid 93 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 103 or (resid 104 thro \ ugh 106 and (name N or name CA or name C or name O or name CB )) or resid 107 th \ rough 109 or (resid 110 through 116 and (name N or name CA or name C or name O o \ r name CB )) or resid 117 or (resid 118 and (name N or name CA or name C or name \ O or name CB )) or resid 119 through 135 or (resid 136 through 137 and (name N \ or name CA or name C or name O or name CB )) or resid 138 through 145 or (resid \ 146 through 147 and (name N or name CA or name C or name O or name CB )) or resi \ d 148 through 164 or (resid 165 through 167 and (name N or name CA or name C or \ name O or name CB )) or resid 168 through 175 or (resid 176 through 177 and (nam \ e N or name CA or name C or name O or name CB )) or resid 178 through 231)) } ncs_group { reference = (chain 'H' and ((resid 29 through 77 and (name N or name CA or name C or name O \ or name CB )) or resid 78 or (resid 79 and (name N or name CA or name C or name \ O or name CB )) or resid 80 through 103 or (resid 104 and (name N or name CA or \ name C or name O or name CB )) or resid 105 or (resid 106 through 108 and (name \ N or name CA or name C or name O or name CB )) or resid 109 through 110 or (resi \ d 111 through 112 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and (resid 29 through 83 or (resid 84 through 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 99 or (resid 100 and (n \ ame N or name CA or name C or name O or name CB )) or resid 101 through 112)) } 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: 99.700 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: 0.050 Extract box with map and model: 1.350 Check model and map are aligned: 0.270 Set scattering table: 0.320 Process input model: 81.210 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.004 0.064 32641 Z= 0.189 Angle : 0.544 8.818 44701 Z= 0.298 Chirality : 0.042 0.306 5517 Planarity : 0.004 0.073 5807 Dihedral : 12.381 89.894 10426 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4765 helix: 2.24 (0.11), residues: 2415 sheet: -1.94 (0.22), residues: 522 loop : -0.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 462 HIS 0.005 0.001 HIS B 396 PHE 0.016 0.001 PHE A 438 TYR 0.021 0.001 TYR A 531 ARG 0.007 0.000 ARG D 223 Details of bonding type rmsd hydrogen bonds : bond 0.15711 ( 2205) hydrogen bonds : angle 6.40500 ( 6522) covalent geometry : bond 0.00373 (32641) covalent geometry : angle 0.54423 (44701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 434 time to evaluate : 3.254 Fit side-chains REVERT: B 161 MET cc_start: 0.8237 (tpp) cc_final: 0.7962 (mmm) REVERT: C 193 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8220 (tp) REVERT: G 90 SER cc_start: 0.8732 (m) cc_final: 0.8350 (m) REVERT: M 61 MET cc_start: 0.8467 (ptt) cc_final: 0.7776 (ppp) outliers start: 9 outliers final: 2 residues processed: 441 average time/residue: 0.4489 time to fit residues: 314.7958 Evaluate side-chains 364 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 361 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 3.9990 chunk 358 optimal weight: 0.5980 chunk 198 optimal weight: 0.0370 chunk 122 optimal weight: 3.9990 chunk 241 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 429 optimal weight: 40.0000 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122801 restraints weight = 39728.458| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.33 r_work: 0.3125 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32641 Z= 0.224 Angle : 0.568 8.682 44701 Z= 0.295 Chirality : 0.044 0.200 5517 Planarity : 0.005 0.054 5807 Dihedral : 4.794 74.841 5131 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.12), residues: 4765 helix: 2.26 (0.11), residues: 2388 sheet: -2.18 (0.21), residues: 508 loop : -0.27 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 462 HIS 0.006 0.001 HIS B 396 PHE 0.022 0.001 PHE B 439 TYR 0.019 0.001 TYR B 49 ARG 0.006 0.001 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 2205) hydrogen bonds : angle 4.95961 ( 6522) covalent geometry : bond 0.00535 (32641) covalent geometry : angle 0.56828 (44701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 404 time to evaluate : 3.560 Fit side-chains revert: symmetry clash REVERT: B 150 MET cc_start: 0.9358 (ttt) cc_final: 0.9145 (ttt) REVERT: B 161 MET cc_start: 0.8526 (tpp) cc_final: 0.8092 (mmm) REVERT: B 387 ILE cc_start: 0.8254 (tp) cc_final: 0.8025 (tp) REVERT: D 391 MET cc_start: 0.6789 (mpp) cc_final: 0.6502 (ptp) REVERT: E 294 LEU cc_start: 0.9067 (mt) cc_final: 0.8842 (mt) REVERT: E 359 ARG cc_start: 0.8522 (mmp80) cc_final: 0.7989 (mmt90) REVERT: F 442 THR cc_start: 0.8669 (m) cc_final: 0.8335 (p) REVERT: G 90 SER cc_start: 0.8968 (m) cc_final: 0.8526 (m) REVERT: K 157 MET cc_start: 0.8565 (mtt) cc_final: 0.8314 (mtt) REVERT: M 61 MET cc_start: 0.8547 (ptt) cc_final: 0.7771 (ppp) outliers start: 24 outliers final: 19 residues processed: 416 average time/residue: 0.4815 time to fit residues: 319.7211 Evaluate side-chains 391 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 372 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 440 optimal weight: 20.0000 chunk 364 optimal weight: 40.0000 chunk 357 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 443 optimal weight: 50.0000 chunk 306 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127590 restraints weight = 39310.168| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.80 r_work: 0.3151 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32641 Z= 0.195 Angle : 0.539 7.119 44701 Z= 0.277 Chirality : 0.043 0.349 5517 Planarity : 0.004 0.065 5807 Dihedral : 4.603 75.289 5128 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 11.86 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.12), residues: 4765 helix: 2.30 (0.11), residues: 2389 sheet: -2.42 (0.21), residues: 510 loop : -0.29 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 462 HIS 0.006 0.001 HIS E 450 PHE 0.019 0.001 PHE B 439 TYR 0.020 0.001 TYR A 531 ARG 0.007 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 2205) hydrogen bonds : angle 4.77168 ( 6522) covalent geometry : bond 0.00465 (32641) covalent geometry : angle 0.53862 (44701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 397 time to evaluate : 3.646 Fit side-chains REVERT: A 610 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7096 (tpt90) REVERT: B 118 ARG cc_start: 0.8658 (mtm110) cc_final: 0.8432 (mtm110) REVERT: B 161 MET cc_start: 0.8639 (tpp) cc_final: 0.8232 (mmm) REVERT: E 294 LEU cc_start: 0.9067 (mt) cc_final: 0.8823 (mt) REVERT: E 378 GLN cc_start: 0.8486 (tt0) cc_final: 0.8280 (tt0) REVERT: F 442 THR cc_start: 0.8712 (m) cc_final: 0.8388 (p) REVERT: G 90 SER cc_start: 0.8966 (m) cc_final: 0.8581 (m) REVERT: K 157 MET cc_start: 0.8475 (mtt) cc_final: 0.8250 (mtt) REVERT: L 90 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7466 (tttt) REVERT: M 40 THR cc_start: 0.8840 (m) cc_final: 0.8508 (m) REVERT: M 61 MET cc_start: 0.8537 (ptt) cc_final: 0.7777 (ppp) outliers start: 40 outliers final: 31 residues processed: 416 average time/residue: 0.4645 time to fit residues: 307.7428 Evaluate side-chains 391 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 360 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 312 MET Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 116 optimal weight: 2.9990 chunk 103 optimal weight: 0.0050 chunk 251 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 438 optimal weight: 40.0000 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 341 optimal weight: 20.0000 chunk 143 optimal weight: 0.9980 chunk 366 optimal weight: 20.0000 chunk 277 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN D 50 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133036 restraints weight = 39069.629| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.64 r_work: 0.3021 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32641 Z= 0.121 Angle : 0.484 7.666 44701 Z= 0.249 Chirality : 0.041 0.190 5517 Planarity : 0.004 0.050 5807 Dihedral : 4.356 75.433 5128 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.77 % Favored : 97.21 % Rotamer: Outliers : 1.80 % Allowed : 13.66 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.13), residues: 4765 helix: 2.46 (0.11), residues: 2397 sheet: -2.31 (0.21), residues: 517 loop : -0.22 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.005 0.001 HIS E 450 PHE 0.017 0.001 PHE B 439 TYR 0.019 0.001 TYR A 531 ARG 0.007 0.000 ARG M 197 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 2205) hydrogen bonds : angle 4.52295 ( 6522) covalent geometry : bond 0.00275 (32641) covalent geometry : angle 0.48394 (44701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 424 time to evaluate : 3.442 Fit side-chains REVERT: A 234 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8832 (mm) REVERT: A 483 ASP cc_start: 0.8598 (m-30) cc_final: 0.8246 (m-30) REVERT: A 610 ARG cc_start: 0.7885 (mmm-85) cc_final: 0.7275 (tpt90) REVERT: B 161 MET cc_start: 0.8416 (tpp) cc_final: 0.8019 (mmm) REVERT: B 384 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8330 (mtmm) REVERT: E 290 MET cc_start: 0.7518 (tpt) cc_final: 0.6965 (tpp) REVERT: E 608 GLN cc_start: 0.8268 (tp40) cc_final: 0.8047 (tp40) REVERT: F 134 ILE cc_start: 0.7591 (pt) cc_final: 0.7343 (pt) REVERT: F 442 THR cc_start: 0.8509 (m) cc_final: 0.8210 (p) REVERT: G 90 SER cc_start: 0.8891 (m) cc_final: 0.8505 (m) REVERT: I 87 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7987 (ttmm) REVERT: I 220 LEU cc_start: 0.8792 (tp) cc_final: 0.8591 (tp) REVERT: K 157 MET cc_start: 0.8436 (mtt) cc_final: 0.8217 (mtt) REVERT: L 90 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7562 (tttt) REVERT: M 40 THR cc_start: 0.8840 (m) cc_final: 0.8548 (m) REVERT: M 61 MET cc_start: 0.8520 (ptt) cc_final: 0.7758 (ppp) outliers start: 43 outliers final: 22 residues processed: 448 average time/residue: 0.4477 time to fit residues: 318.7837 Evaluate side-chains 402 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 24 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 362 optimal weight: 10.0000 chunk 395 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 339 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 448 optimal weight: 30.0000 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN B 396 HIS ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.161136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125423 restraints weight = 39102.189| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.80 r_work: 0.2911 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 32641 Z= 0.285 Angle : 0.603 10.118 44701 Z= 0.309 Chirality : 0.046 0.433 5517 Planarity : 0.005 0.064 5807 Dihedral : 4.580 75.927 5126 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 3.18 % Allowed : 14.54 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.12), residues: 4765 helix: 2.29 (0.11), residues: 2391 sheet: -2.45 (0.21), residues: 509 loop : -0.40 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 541 HIS 0.006 0.002 HIS A 213 PHE 0.022 0.002 PHE B 439 TYR 0.020 0.002 TYR B 49 ARG 0.008 0.001 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 2205) hydrogen bonds : angle 4.73479 ( 6522) covalent geometry : bond 0.00692 (32641) covalent geometry : angle 0.60288 (44701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 3.383 Fit side-chains REVERT: A 234 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8942 (mm) REVERT: A 610 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7220 (tpt90) REVERT: B 118 ARG cc_start: 0.8628 (mtm110) cc_final: 0.8395 (mtm110) REVERT: B 161 MET cc_start: 0.8736 (tpp) cc_final: 0.8203 (mmm) REVERT: B 384 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8418 (mtmm) REVERT: C 478 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7821 (t80) REVERT: D 276 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9004 (m) REVERT: D 450 GLU cc_start: 0.8076 (tt0) cc_final: 0.7815 (tt0) REVERT: E 290 MET cc_start: 0.7629 (tpt) cc_final: 0.6940 (tpp) REVERT: E 294 LEU cc_start: 0.9017 (mt) cc_final: 0.8732 (mt) REVERT: E 359 ARG cc_start: 0.8497 (mmp80) cc_final: 0.8018 (mmt90) REVERT: E 608 GLN cc_start: 0.8434 (tp40) cc_final: 0.8230 (tp40) REVERT: F 442 THR cc_start: 0.8678 (m) cc_final: 0.8342 (p) REVERT: G 90 SER cc_start: 0.9014 (m) cc_final: 0.8592 (m) REVERT: G 144 ARG cc_start: 0.8734 (ptt90) cc_final: 0.8445 (ptt90) REVERT: I 87 LYS cc_start: 0.8309 (ttmm) cc_final: 0.7978 (ttmm) REVERT: I 127 GLU cc_start: 0.8587 (tt0) cc_final: 0.8135 (tt0) REVERT: I 149 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7933 (mt) REVERT: L 90 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7462 (tttt) REVERT: M 40 THR cc_start: 0.8816 (m) cc_final: 0.8488 (m) REVERT: M 61 MET cc_start: 0.8565 (ptt) cc_final: 0.7832 (ppp) outliers start: 76 outliers final: 51 residues processed: 427 average time/residue: 0.4561 time to fit residues: 307.4771 Evaluate side-chains 410 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 354 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 37 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 455 optimal weight: 50.0000 chunk 223 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 358 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN C 346 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.164021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127207 restraints weight = 39049.998| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.34 r_work: 0.3053 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32641 Z= 0.158 Angle : 0.515 9.505 44701 Z= 0.263 Chirality : 0.042 0.339 5517 Planarity : 0.004 0.053 5807 Dihedral : 4.404 74.925 5126 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.06 % Rotamer: Outliers : 2.81 % Allowed : 16.13 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4765 helix: 2.43 (0.11), residues: 2386 sheet: -2.43 (0.21), residues: 506 loop : -0.33 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.006 0.001 HIS E 450 PHE 0.018 0.001 PHE B 439 TYR 0.018 0.001 TYR B 49 ARG 0.008 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 2205) hydrogen bonds : angle 4.55894 ( 6522) covalent geometry : bond 0.00369 (32641) covalent geometry : angle 0.51519 (44701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 380 time to evaluate : 3.309 Fit side-chains revert: symmetry clash REVERT: A 234 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8910 (mm) REVERT: A 610 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7251 (tpt90) REVERT: B 118 ARG cc_start: 0.8617 (mtm110) cc_final: 0.8380 (mtm110) REVERT: B 161 MET cc_start: 0.8600 (tpp) cc_final: 0.8101 (mmm) REVERT: B 383 MET cc_start: 0.8119 (ttp) cc_final: 0.7810 (ttt) REVERT: B 384 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: D 276 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8975 (m) REVERT: D 416 MET cc_start: 0.7635 (tpp) cc_final: 0.7281 (tpt) REVERT: D 450 GLU cc_start: 0.8058 (tt0) cc_final: 0.7785 (tt0) REVERT: E 312 MET cc_start: 0.8389 (tpt) cc_final: 0.8141 (tpt) REVERT: E 359 ARG cc_start: 0.8392 (mmp80) cc_final: 0.7924 (mmt90) REVERT: F 442 THR cc_start: 0.8629 (m) cc_final: 0.8318 (p) REVERT: G 90 SER cc_start: 0.8947 (m) cc_final: 0.8523 (m) REVERT: I 87 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8066 (ttmm) REVERT: I 127 GLU cc_start: 0.8527 (tt0) cc_final: 0.8102 (tt0) REVERT: K 166 ARG cc_start: 0.9239 (ptp-170) cc_final: 0.8907 (ptp-170) REVERT: M 40 THR cc_start: 0.8782 (m) cc_final: 0.8468 (m) REVERT: M 61 MET cc_start: 0.8565 (ptt) cc_final: 0.7827 (ppp) outliers start: 67 outliers final: 41 residues processed: 421 average time/residue: 0.4367 time to fit residues: 293.7804 Evaluate side-chains 407 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 306 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 369 optimal weight: 2.9990 chunk 411 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN F 339 ASN ** F 344 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.160869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124996 restraints weight = 39464.571| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.62 r_work: 0.2869 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 32641 Z= 0.280 Angle : 0.597 9.770 44701 Z= 0.305 Chirality : 0.045 0.189 5517 Planarity : 0.004 0.062 5807 Dihedral : 4.575 75.348 5126 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 2.81 % Allowed : 16.46 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.13), residues: 4765 helix: 2.27 (0.11), residues: 2393 sheet: -2.58 (0.20), residues: 521 loop : -0.43 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.006 0.002 HIS A 213 PHE 0.021 0.002 PHE B 439 TYR 0.017 0.002 TYR B 49 ARG 0.008 0.001 ARG M 197 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 2205) hydrogen bonds : angle 4.69473 ( 6522) covalent geometry : bond 0.00679 (32641) covalent geometry : angle 0.59694 (44701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 369 time to evaluate : 4.809 Fit side-chains REVERT: A 234 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8952 (mm) REVERT: A 610 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7191 (tpt90) REVERT: B 118 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8376 (mtm110) REVERT: B 161 MET cc_start: 0.8723 (tpp) cc_final: 0.8204 (mmm) REVERT: B 342 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 384 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: C 87 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8289 (mtm110) REVERT: D 276 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8989 (m) REVERT: D 416 MET cc_start: 0.7628 (tpp) cc_final: 0.7316 (tpt) REVERT: E 435 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8413 (m) REVERT: F 339 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: F 442 THR cc_start: 0.8645 (m) cc_final: 0.8296 (p) REVERT: G 90 SER cc_start: 0.8997 (m) cc_final: 0.8581 (m) REVERT: I 87 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7983 (ttmm) REVERT: I 134 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8495 (mt-10) REVERT: I 149 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.8009 (mt) REVERT: K 166 ARG cc_start: 0.9212 (ptp-170) cc_final: 0.8900 (ptp-170) REVERT: M 40 THR cc_start: 0.8803 (m) cc_final: 0.8457 (m) REVERT: M 61 MET cc_start: 0.8596 (ptt) cc_final: 0.7882 (ppp) outliers start: 67 outliers final: 46 residues processed: 415 average time/residue: 0.4507 time to fit residues: 297.4432 Evaluate side-chains 411 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 183 optimal weight: 0.9980 chunk 362 optimal weight: 20.0000 chunk 287 optimal weight: 0.9990 chunk 471 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 270 optimal weight: 0.7980 chunk 393 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 438 optimal weight: 50.0000 chunk 354 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 527 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126157 restraints weight = 39222.820| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.59 r_work: 0.2937 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32641 Z= 0.225 Angle : 0.568 11.175 44701 Z= 0.290 Chirality : 0.044 0.309 5517 Planarity : 0.004 0.055 5807 Dihedral : 4.541 75.060 5126 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 2.76 % Allowed : 17.05 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4765 helix: 2.30 (0.11), residues: 2390 sheet: -2.60 (0.20), residues: 529 loop : -0.42 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.006 0.001 HIS C 170 PHE 0.020 0.001 PHE B 439 TYR 0.017 0.001 TYR B 49 ARG 0.009 0.001 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 2205) hydrogen bonds : angle 4.64554 ( 6522) covalent geometry : bond 0.00543 (32641) covalent geometry : angle 0.56760 (44701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 370 time to evaluate : 3.962 Fit side-chains REVERT: A 234 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 610 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7148 (tpt90) REVERT: B 118 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8402 (mtm110) REVERT: B 161 MET cc_start: 0.8687 (tpp) cc_final: 0.8207 (mmm) REVERT: B 215 MET cc_start: 0.9280 (mtm) cc_final: 0.8980 (mpp) REVERT: B 383 MET cc_start: 0.8240 (ttp) cc_final: 0.7928 (ttt) REVERT: B 384 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: C 87 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8306 (mtm110) REVERT: D 276 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8941 (m) REVERT: E 290 MET cc_start: 0.7539 (tpt) cc_final: 0.7015 (tpp) REVERT: E 435 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8343 (m) REVERT: F 339 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8351 (m-40) REVERT: F 442 THR cc_start: 0.8643 (m) cc_final: 0.8309 (p) REVERT: G 90 SER cc_start: 0.9016 (m) cc_final: 0.8596 (m) REVERT: G 144 ARG cc_start: 0.8738 (ptt90) cc_final: 0.8339 (ptt90) REVERT: I 87 LYS cc_start: 0.8308 (ttmm) cc_final: 0.8015 (ttmm) REVERT: I 149 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8049 (mt) REVERT: K 166 ARG cc_start: 0.9195 (ptp-170) cc_final: 0.8877 (ptp-170) REVERT: M 40 THR cc_start: 0.8788 (m) cc_final: 0.8460 (m) REVERT: M 61 MET cc_start: 0.8584 (ptt) cc_final: 0.7862 (ppp) outliers start: 66 outliers final: 52 residues processed: 417 average time/residue: 0.4673 time to fit residues: 313.7676 Evaluate side-chains 417 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 428 THR Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 381 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 426 optimal weight: 30.0000 chunk 183 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 449 optimal weight: 5.9990 chunk 435 optimal weight: 9.9990 chunk 282 optimal weight: 1.9990 chunk 470 optimal weight: 3.9990 chunk 472 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127167 restraints weight = 39112.623| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.73 r_work: 0.2906 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32641 Z= 0.172 Angle : 0.539 10.717 44701 Z= 0.274 Chirality : 0.043 0.294 5517 Planarity : 0.004 0.054 5807 Dihedral : 4.452 75.301 5126 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 2.64 % Allowed : 17.26 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4765 helix: 2.38 (0.11), residues: 2391 sheet: -2.55 (0.20), residues: 532 loop : -0.36 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 541 HIS 0.006 0.001 HIS C 170 PHE 0.018 0.001 PHE B 439 TYR 0.017 0.001 TYR B 49 ARG 0.008 0.000 ARG M 197 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 2205) hydrogen bonds : angle 4.55938 ( 6522) covalent geometry : bond 0.00411 (32641) covalent geometry : angle 0.53911 (44701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 372 time to evaluate : 3.679 Fit side-chains REVERT: A 234 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 610 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7211 (tpt90) REVERT: B 118 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8434 (mtm110) REVERT: B 161 MET cc_start: 0.8668 (tpp) cc_final: 0.8204 (mmm) REVERT: B 215 MET cc_start: 0.9279 (mtm) cc_final: 0.8993 (mpp) REVERT: B 342 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 383 MET cc_start: 0.8153 (ttp) cc_final: 0.7869 (tpp) REVERT: B 384 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8319 (mtmm) REVERT: C 87 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8276 (mtm110) REVERT: D 276 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8928 (m) REVERT: D 416 MET cc_start: 0.7581 (tpp) cc_final: 0.7224 (tpt) REVERT: E 290 MET cc_start: 0.7495 (tpt) cc_final: 0.6894 (tpp) REVERT: E 334 TYR cc_start: 0.9094 (m-80) cc_final: 0.8769 (m-80) REVERT: E 435 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8308 (m) REVERT: F 339 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: F 442 THR cc_start: 0.8658 (m) cc_final: 0.8321 (p) REVERT: G 90 SER cc_start: 0.8940 (m) cc_final: 0.8516 (m) REVERT: G 144 ARG cc_start: 0.8714 (ptt90) cc_final: 0.8261 (ptt90) REVERT: I 87 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8065 (ttmm) REVERT: I 127 GLU cc_start: 0.8560 (tt0) cc_final: 0.8079 (tt0) REVERT: I 149 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7964 (mt) REVERT: K 92 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8430 (mtt-85) REVERT: K 153 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8061 (ttmt) REVERT: K 166 ARG cc_start: 0.9187 (ptp-170) cc_final: 0.8870 (ptp-170) REVERT: K 176 ASN cc_start: 0.8326 (t0) cc_final: 0.8115 (m-40) REVERT: M 40 THR cc_start: 0.8816 (m) cc_final: 0.8481 (m) REVERT: M 61 MET cc_start: 0.8600 (ptt) cc_final: 0.7876 (ppp) outliers start: 63 outliers final: 49 residues processed: 415 average time/residue: 0.4606 time to fit residues: 304.4397 Evaluate side-chains 424 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 367 time to evaluate : 4.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 136 LYS Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 0.3980 chunk 48 optimal weight: 0.0570 chunk 352 optimal weight: 3.9990 chunk 304 optimal weight: 2.9990 chunk 284 optimal weight: 0.4980 chunk 381 optimal weight: 0.7980 chunk 245 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131200 restraints weight = 38782.728| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.90 r_work: 0.3240 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32641 Z= 0.128 Angle : 0.509 13.217 44701 Z= 0.259 Chirality : 0.042 0.362 5517 Planarity : 0.004 0.054 5807 Dihedral : 4.323 75.156 5126 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.83 % Favored : 97.15 % Rotamer: Outliers : 2.22 % Allowed : 17.76 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4765 helix: 2.50 (0.11), residues: 2396 sheet: -2.45 (0.21), residues: 522 loop : -0.30 (0.15), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.005 0.001 HIS C 170 PHE 0.017 0.001 PHE B 439 TYR 0.015 0.001 TYR B 49 ARG 0.007 0.000 ARG D 118 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 2205) hydrogen bonds : angle 4.43455 ( 6522) covalent geometry : bond 0.00293 (32641) covalent geometry : angle 0.50912 (44701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9530 Ramachandran restraints generated. 4765 Oldfield, 0 Emsley, 4765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 391 time to evaluate : 3.485 Fit side-chains revert: symmetry clash REVERT: A 234 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8906 (mm) REVERT: A 610 ARG cc_start: 0.7793 (mmm-85) cc_final: 0.7147 (tpt90) REVERT: B 118 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8348 (mtm110) REVERT: B 161 MET cc_start: 0.8545 (tpp) cc_final: 0.8156 (mmm) REVERT: B 215 MET cc_start: 0.9231 (mtm) cc_final: 0.8864 (mpp) REVERT: B 307 TYR cc_start: 0.9008 (p90) cc_final: 0.8647 (p90) REVERT: B 352 TYR cc_start: 0.8876 (m-80) cc_final: 0.8462 (m-80) REVERT: B 384 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8242 (mtmm) REVERT: C 87 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8313 (mtm110) REVERT: C 300 LEU cc_start: 0.8034 (mt) cc_final: 0.7754 (mt) REVERT: D 276 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8863 (m) REVERT: E 334 TYR cc_start: 0.9019 (m-80) cc_final: 0.8755 (m-80) REVERT: E 435 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (m) REVERT: F 134 ILE cc_start: 0.7555 (pt) cc_final: 0.7246 (pt) REVERT: F 339 ASN cc_start: 0.8523 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: F 442 THR cc_start: 0.8588 (m) cc_final: 0.8284 (p) REVERT: G 144 ARG cc_start: 0.8642 (ptt90) cc_final: 0.8316 (ptt90) REVERT: I 118 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8400 (tttm) REVERT: I 127 GLU cc_start: 0.8391 (tt0) cc_final: 0.8034 (tt0) REVERT: I 149 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7631 (mt) REVERT: K 110 ILE cc_start: 0.9068 (mm) cc_final: 0.8787 (mm) REVERT: K 166 ARG cc_start: 0.9132 (ptp-170) cc_final: 0.8790 (ptp-170) REVERT: L 91 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7604 (ttmm) REVERT: M 40 THR cc_start: 0.8836 (m) cc_final: 0.8523 (m) REVERT: M 61 MET cc_start: 0.8576 (ptt) cc_final: 0.7811 (ppp) outliers start: 53 outliers final: 41 residues processed: 425 average time/residue: 0.4647 time to fit residues: 313.7076 Evaluate side-chains 419 residues out of total 4135 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 371 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 311 ILE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 339 ASN Chi-restraints excluded: chain F residue 453 THR Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 390 optimal weight: 10.0000 chunk 168 optimal weight: 0.0020 chunk 206 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 295 optimal weight: 0.0870 chunk 250 optimal weight: 0.8980 chunk 324 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 426 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 overall best weight: 0.7970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN F 27 ASN F 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.164655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131486 restraints weight = 38954.505| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.69 r_work: 0.2969 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32641 Z= 0.160 Angle : 0.525 13.314 44701 Z= 0.266 Chirality : 0.042 0.391 5517 Planarity : 0.004 0.054 5807 Dihedral : 4.335 75.324 5126 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 2.56 % Allowed : 17.43 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4765 helix: 2.49 (0.11), residues: 2396 sheet: -2.42 (0.21), residues: 519 loop : -0.31 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.005 0.001 HIS C 170 PHE 0.017 0.001 PHE B 439 TYR 0.016 0.001 TYR F 370 ARG 0.007 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 2205) hydrogen bonds : angle 4.43952 ( 6522) covalent geometry : bond 0.00378 (32641) covalent geometry : angle 0.52507 (44701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19383.06 seconds wall clock time: 335 minutes 54.71 seconds (20154.71 seconds total)