Starting phenix.real_space_refine on Tue Aug 26 16:52:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.cif Found real_map, /net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.map" model { file = "/net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9its_60877/08_2025/9its_60877.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 14 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 24906 2.51 5 N 6919 2.21 5 O 7447 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39399 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3775 Classifications: {'peptide': 496} Link IDs: {'PTRANS': 25, 'TRANS': 470} Chain: "B" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3838 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 26, 'TRANS': 477} Chain: "C" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 26, 'TRANS': 493} Chain: "D" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3638 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 28, 'TRANS': 442} Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3632 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 442} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3615 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 441} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2249 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain: "R" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1014 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "S" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 549 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "Y" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1223 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 1, 'TRANS': 151} Chain: "V" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1230 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "W" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 538 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "U" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 772 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 3, 'GLN:plan1': 12, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 292 Chain: "X" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 758 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PTRANS': 1, 'TRANS': 150} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 582 Unresolved non-hydrogen dihedrals: 364 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 12, 'ASN:plan1': 4, 'ARG:plan': 20, 'TYR:plan': 2, 'GLU:plan': 20, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 289 Chain: "H" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 506 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "J" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "K" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "N" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "O" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "Q" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 517 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "T" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 1310 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'PTRANS': 15, 'TRANS': 250} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 825 Unresolved non-hydrogen angles: 1078 Unresolved non-hydrogen dihedrals: 696 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 34, 'TYR:plan': 7, 'HIS:plan': 3, 'GLU:plan': 12, 'ASP:plan': 4, 'ASN:plan1': 12, 'GLN:plan1': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 433 Chain: "Z" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1984 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.85, per 1000 atoms: 0.25 Number of scatterers: 39399 At special positions: 0 Unit cell: (134.85, 148.8, 234.36, 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 108 16.00 P 14 15.00 Mg 5 11.99 O 7447 8.00 N 6919 7.00 C 24906 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: 3.50 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9766 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 28 sheets defined 58.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.631A pdb=" N LEU A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.583A pdb=" N GLN A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 226 removed outlier: 3.832A pdb=" N GLU A 226 " --> pdb=" O GLY A 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 244 through 259 Processing helix chain 'A' and resid 277 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.678A pdb=" N GLY A 324 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.632A pdb=" N THR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 Processing helix chain 'A' and resid 387 through 407 removed outlier: 4.725A pdb=" N LYS A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 3.752A pdb=" N ARG A 487 " --> pdb=" O HIS A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.673A pdb=" N LEU B 110 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.570A pdb=" N GLN B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.576A pdb=" N GLU B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 246 through 260 removed outlier: 6.110A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.722A pdb=" N ALA B 300 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.703A pdb=" N ALA B 384 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 407 removed outlier: 3.679A pdb=" N GLY B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LYS B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.522A pdb=" N ALA B 411 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 412 " --> pdb=" O ALA B 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 408 through 412' Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 444 through 457 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 482 Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.893A pdb=" N ARG B 487 " --> pdb=" O HIS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.540A pdb=" N GLY C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 181 through 192 Processing helix chain 'C' and resid 208 through 222 Processing helix chain 'C' and resid 223 through 226 removed outlier: 3.549A pdb=" N GLU C 226 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 238 through 259 Proline residue: C 246 - end of helix Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 302 through 303 No H-bonds generated for 'chain 'C' and resid 302 through 303' Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.621A pdb=" N LEU C 312 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.598A pdb=" N GLY C 324 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 360 through 365 Processing helix chain 'C' and resid 381 through 386 removed outlier: 3.781A pdb=" N ALA C 384 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.942A pdb=" N GLY C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 411 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 483 through 493 removed outlier: 3.783A pdb=" N ARG C 487 " --> pdb=" O HIS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 518 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 222 through 243 removed outlier: 4.768A pdb=" N GLY D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.544A pdb=" N LEU D 325 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 387 removed outlier: 3.677A pdb=" N ASP D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 Processing helix chain 'D' and resid 429 through 442 removed outlier: 3.675A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.506A pdb=" N VAL D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 192 through 201 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 222 through 243 removed outlier: 3.506A pdb=" N ARG E 226 " --> pdb=" O PRO E 222 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY E 230 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE E 240 " --> pdb=" O MET E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 268 Processing helix chain 'E' and resid 280 through 290 removed outlier: 3.651A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 362 through 387 removed outlier: 5.402A pdb=" N GLN E 368 " --> pdb=" O TYR E 364 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 459 through 470 removed outlier: 3.601A pdb=" N LEU E 463 " --> pdb=" O PHE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.233A pdb=" N VAL F 24 " --> pdb=" O GLU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 158 through 171 Processing helix chain 'F' and resid 193 through 199 Processing helix chain 'F' and resid 222 through 243 removed outlier: 3.567A pdb=" N ARG F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY F 230 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE F 240 " --> pdb=" O MET F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 268 removed outlier: 3.781A pdb=" N PHE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 315 through 323 removed outlier: 4.177A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 360 through 387 removed outlier: 4.834A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE F 383 " --> pdb=" O ASP F 379 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 392 removed outlier: 3.799A pdb=" N GLU F 391 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.936A pdb=" N GLN F 418 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 removed outlier: 3.552A pdb=" N GLY F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.537A pdb=" N TYR F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.542A pdb=" N VAL F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 60 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 93 through 112 Processing helix chain 'G' and resid 122 through 133 removed outlier: 3.531A pdb=" N ARG G 126 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY G 133 " --> pdb=" O PHE G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 165 removed outlier: 3.860A pdb=" N ILE G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 287 Proline residue: G 222 - end of helix Processing helix chain 'R' and resid 92 through 101 removed outlier: 3.683A pdb=" N ALA R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 124 Processing helix chain 'S' and resid 98 through 110 Processing helix chain 'S' and resid 143 through 154 Processing helix chain 'Y' and resid 9 through 147 removed outlier: 5.504A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix Processing helix chain 'Y' and resid 149 through 160 Processing helix chain 'V' and resid 7 through 27 Processing helix chain 'V' and resid 29 through 114 removed outlier: 3.529A pdb=" N GLN V 112 " --> pdb=" O GLU V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 121 Processing helix chain 'V' and resid 122 through 136 removed outlier: 4.020A pdb=" N SER V 126 " --> pdb=" O SER V 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE V 128 " --> pdb=" O ALA V 124 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA V 129 " --> pdb=" O LYS V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 157 removed outlier: 4.130A pdb=" N LEU V 152 " --> pdb=" O GLY V 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 98 through 109 removed outlier: 3.530A pdb=" N LEU W 109 " --> pdb=" O ILE W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 112 No H-bonds generated for 'chain 'W' and resid 110 through 112' Processing helix chain 'W' and resid 123 through 127 removed outlier: 3.927A pdb=" N ILE W 127 " --> pdb=" O PRO W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 147 Processing helix chain 'U' and resid 7 through 122 removed outlier: 3.692A pdb=" N PHE U 11 " --> pdb=" O ASN U 7 " (cutoff:3.500A) Proline residue: U 32 - end of helix removed outlier: 3.823A pdb=" N SER U 122 " --> pdb=" O ILE U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 122 through 127 removed outlier: 3.975A pdb=" N SER U 126 " --> pdb=" O SER U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 140 removed outlier: 3.692A pdb=" N LEU U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 155 removed outlier: 4.490A pdb=" N ALA U 154 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 131 Proline residue: X 32 - end of helix removed outlier: 3.641A pdb=" N ALA X 129 " --> pdb=" O LYS X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 147 removed outlier: 3.937A pdb=" N ARG X 138 " --> pdb=" O LEU X 134 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL X 139 " --> pdb=" O THR X 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 38 removed outlier: 4.430A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) Proline residue: H 20 - end of helix Processing helix chain 'H' and resid 41 through 72 Processing helix chain 'I' and resid 3 through 38 Proline residue: I 20 - end of helix Processing helix chain 'I' and resid 41 through 73 removed outlier: 4.035A pdb=" N ALA I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 41 through 72 Processing helix chain 'K' and resid 3 through 38 removed outlier: 3.906A pdb=" N GLY K 19 " --> pdb=" O LEU K 15 " (cutoff:3.500A) Proline residue: K 20 - end of helix Processing helix chain 'K' and resid 41 through 72 removed outlier: 4.411A pdb=" N ALA K 67 " --> pdb=" O GLY K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 14 removed outlier: 3.879A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 18 through 37 removed outlier: 3.866A pdb=" N ARG L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 41 through 72 removed outlier: 3.712A pdb=" N VAL L 46 " --> pdb=" O GLU L 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.240A pdb=" N THR M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR M 48 " --> pdb=" O ARG M 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 38 removed outlier: 4.034A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Proline residue: N 20 - end of helix Processing helix chain 'N' and resid 41 through 72 removed outlier: 3.832A pdb=" N GLU N 57 " --> pdb=" O ILE N 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE N 72 " --> pdb=" O PHE N 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 38 removed outlier: 3.511A pdb=" N THR O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) Proline residue: O 20 - end of helix Processing helix chain 'O' and resid 41 through 73 removed outlier: 4.297A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 18 through 38 removed outlier: 3.570A pdb=" N VAL P 22 " --> pdb=" O ILE P 18 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 4.411A pdb=" N THR P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 Proline residue: Q 20 - end of helix Processing helix chain 'Q' and resid 41 through 72 removed outlier: 4.924A pdb=" N THR Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.521A pdb=" N VAL T 53 " --> pdb=" O THR T 49 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL T 54 " --> pdb=" O ASN T 50 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 99 removed outlier: 3.630A pdb=" N ILE T 98 " --> pdb=" O LEU T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 124 removed outlier: 3.724A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 171 through 178 removed outlier: 3.504A pdb=" N ALA T 174 " --> pdb=" O ASP T 171 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA T 175 " --> pdb=" O THR T 172 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN T 176 " --> pdb=" O CYS T 173 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY T 177 " --> pdb=" O ALA T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 186 through 189 Processing helix chain 'T' and resid 190 through 212 removed outlier: 3.638A pdb=" N THR T 194 " --> pdb=" O ASP T 190 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA T 212 " --> pdb=" O TRP T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 221 removed outlier: 3.736A pdb=" N LYS T 219 " --> pdb=" O PRO T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 268 removed outlier: 3.743A pdb=" N VAL T 231 " --> pdb=" O ILE T 227 " (cutoff:3.500A) Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 273 through 304 removed outlier: 3.619A pdb=" N PHE T 285 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA T 292 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 21 removed outlier: 3.893A pdb=" N ALA Z 20 " --> pdb=" O ILE Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 3.502A pdb=" N VAL Z 53 " --> pdb=" O THR Z 49 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL Z 54 " --> pdb=" O ASN Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 99 removed outlier: 3.893A pdb=" N ILE Z 87 " --> pdb=" O VAL Z 83 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU Z 88 " --> pdb=" O MET Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Proline residue: Z 108 - end of helix removed outlier: 3.940A pdb=" N VAL Z 117 " --> pdb=" O ILE Z 113 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU Z 125 " --> pdb=" O ASN Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 214 removed outlier: 3.689A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 220 removed outlier: 3.854A pdb=" N LYS Z 219 " --> pdb=" O PRO Z 215 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 268 removed outlier: 3.593A pdb=" N ILE Z 234 " --> pdb=" O PHE Z 230 " (cutoff:3.500A) Proline residue: Z 243 - end of helix removed outlier: 3.706A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 273 through 304 removed outlier: 3.918A pdb=" N PHE Z 285 " --> pdb=" O VAL Z 281 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 31 current: chain 'A' and resid 67 through 74 removed outlier: 4.422A pdb=" N TYR A 67 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 79 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 73 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 83 current: chain 'F' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 14 through 18 current: chain 'F' and resid 41 through 48 removed outlier: 6.817A pdb=" N LYS F 55 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLN F 48 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 53 " --> pdb=" O GLN F 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 4.385A pdb=" N LYS A 132 " --> pdb=" O VAL A 106 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.598A pdb=" N ILE A 166 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 335 removed outlier: 8.079A pdb=" N ILE A 334 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 174 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 173 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU A 359 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 175 " --> pdb=" O LEU A 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 39 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 41 current: chain 'B' and resid 68 through 74 removed outlier: 5.435A pdb=" N ALA B 70 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 81 " --> pdb=" O ALA B 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 82 current: chain 'D' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 14 through 18 current: chain 'D' and resid 40 through 49 removed outlier: 6.863A pdb=" N LYS D 55 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN D 48 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 53 " --> pdb=" O GLN D 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 57 current: chain 'W' and resid 119 through 121 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 119 through 121 current: chain 'W' and resid 137 through 140 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 4.233A pdb=" N LYS B 132 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.670A pdb=" N CYS B 200 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 231 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR B 202 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA B 233 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA B 204 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 335 removed outlier: 6.457A pdb=" N ILE B 174 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 261 through 263 Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 35 removed outlier: 3.575A pdb=" N ALA C 34 " --> pdb=" O ARG C 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 39 through 42 current: chain 'C' and resid 68 through 74 removed outlier: 5.630A pdb=" N ALA C 70 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE C 81 " --> pdb=" O ALA C 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 77 through 82 current: chain 'E' and resid 14 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 14 through 18 current: chain 'E' and resid 40 through 48 removed outlier: 6.579A pdb=" N LYS E 55 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN E 48 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 53 " --> pdb=" O GLN E 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 53 through 57 current: chain 'S' and resid 137 through 139 Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 106 removed outlier: 4.302A pdb=" N LYS C 132 " --> pdb=" O VAL C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.498A pdb=" N ALA C 271 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 331 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE C 273 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL C 333 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 275 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU C 335 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU C 172 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE C 334 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 174 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR C 336 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 176 " --> pdb=" O THR C 336 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 261 through 263 Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 82 removed outlier: 4.187A pdb=" N GLU D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.395A pdb=" N ILE D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N MET D 303 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 249 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR D 149 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL D 306 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 151 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 327 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 129 through 130 removed outlier: 4.213A pdb=" N PHE D 143 " --> pdb=" O PHE D 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC2, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.409A pdb=" N PHE E 91 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLN E 218 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 179 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N MET E 303 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 249 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR E 149 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS E 148 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE E 329 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA E 150 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 129 through 130 removed outlier: 4.163A pdb=" N PHE E 143 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 79 through 81 Processing sheet with id=AC5, first strand: chain 'F' and resid 90 through 91 removed outlier: 8.952A pdb=" N VAL F 213 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER F 178 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL F 215 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE F 180 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET F 303 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU F 249 " --> pdb=" O MET F 303 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR F 149 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL F 306 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE F 151 " --> pdb=" O VAL F 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 129 through 130 removed outlier: 4.158A pdb=" N PHE F 143 " --> pdb=" O PHE F 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 202 through 203 Processing sheet with id=AC8, first strand: chain 'G' and resid 138 through 140 removed outlier: 4.085A pdb=" N GLY G 138 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL G 79 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU G 81 " --> pdb=" O TYR G 119 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE G 121 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 83 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER G 176 " --> pdb=" O VAL G 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 208 through 209 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 208 through 209 current: chain 'R' and resid 13 through 19 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 13 through 19 current: chain 'R' and resid 58 through 70 Processing sheet with id=AD1, first strand: chain 'Z' and resid 133 through 136 2409 hydrogen bonds defined for protein. 7053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.01 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13321 1.34 - 1.46: 4114 1.46 - 1.57: 22300 1.57 - 1.69: 21 1.69 - 1.81: 205 Bond restraints: 39961 Sorted by residual: bond pdb=" N ILE W 150 " pdb=" CA ILE W 150 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.60e+00 bond pdb=" O4 PO4 D 502 " pdb=" P PO4 D 502 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" O3 PO4 D 502 " pdb=" P PO4 D 502 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.44e+00 bond pdb=" O2 PO4 D 502 " pdb=" P PO4 D 502 " ideal model delta sigma weight residual 1.567 1.507 0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" N ASP A 277 " pdb=" CA ASP A 277 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.37e+00 ... (remaining 39956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 53531 2.05 - 4.11: 646 4.11 - 6.16: 104 6.16 - 8.21: 17 8.21 - 10.27: 3 Bond angle restraints: 54301 Sorted by residual: angle pdb=" N ILE R 87 " pdb=" CA ILE R 87 " pdb=" C ILE R 87 " ideal model delta sigma weight residual 111.62 108.19 3.43 7.90e-01 1.60e+00 1.88e+01 angle pdb=" N LEU W 147 " pdb=" CA LEU W 147 " pdb=" C LEU W 147 " ideal model delta sigma weight residual 113.18 108.18 5.00 1.21e+00 6.83e-01 1.71e+01 angle pdb=" N ARG R 127 " pdb=" CA ARG R 127 " pdb=" C ARG R 127 " ideal model delta sigma weight residual 113.23 108.30 4.93 1.24e+00 6.50e-01 1.58e+01 angle pdb=" C ALA R 129 " pdb=" CA ALA R 129 " pdb=" CB ALA R 129 " ideal model delta sigma weight residual 117.23 111.82 5.41 1.36e+00 5.41e-01 1.58e+01 angle pdb=" N GLN V 115 " pdb=" CA GLN V 115 " pdb=" C GLN V 115 " ideal model delta sigma weight residual 113.20 108.76 4.44 1.21e+00 6.83e-01 1.35e+01 ... (remaining 54296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.07: 23636 33.07 - 66.14: 486 66.14 - 99.22: 44 99.22 - 132.29: 0 132.29 - 165.36: 1 Dihedral angle restraints: 24167 sinusoidal: 8956 harmonic: 15211 Sorted by residual: dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual 300.00 134.64 165.36 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" CA TYR E 364 " pdb=" C TYR E 364 " pdb=" N ARG E 365 " pdb=" CA ARG E 365 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG C 369 " pdb=" C ARG C 369 " pdb=" N PRO C 370 " pdb=" CA PRO C 370 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 24164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5304 0.057 - 0.115: 989 0.115 - 0.172: 136 0.172 - 0.230: 9 0.230 - 0.287: 1 Chirality restraints: 6439 Sorted by residual: chirality pdb=" CB ILE A 53 " pdb=" CA ILE A 53 " pdb=" CG1 ILE A 53 " pdb=" CG2 ILE A 53 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE R 52 " pdb=" CA ILE R 52 " pdb=" CG1 ILE R 52 " pdb=" CG2 ILE R 52 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASP A 277 " pdb=" N ASP A 277 " pdb=" C ASP A 277 " pdb=" CB ASP A 277 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 6436 not shown) Planarity restraints: 7149 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 53 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C ILE L 53 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE L 53 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA L 54 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY M 19 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO M 20 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO M 20 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO M 20 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO A 117 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.033 5.00e-02 4.00e+02 ... (remaining 7146 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 267 2.56 - 3.14: 32023 3.14 - 3.73: 65160 3.73 - 4.31: 87516 4.31 - 4.90: 147790 Nonbonded interactions: 332756 Sorted by model distance: nonbonded pdb=" OG1 THR B 183 " pdb="MG MG B 601 " model vdw 1.973 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1G ATP B 602 " model vdw 1.990 2.170 nonbonded pdb=" OG1 THR C 183 " pdb="MG MG C 601 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR A 183 " pdb="MG MG A 601 " model vdw 2.013 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1G ATP C 602 " model vdw 2.018 2.170 ... (remaining 332751 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 27 through 521 or resid 601 through 602)) selection = (chain 'B' and resid 27 through 602) selection = (chain 'C' and resid 27 through 602) } ncs_group { reference = (chain 'D' and (resid 2 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 470)) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } ncs_group { reference = chain 'H' selection = (chain 'I' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'J' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'K' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'L' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'M' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'N' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'O' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'P' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) selection = (chain 'Q' and ((resid 1 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 72)) } ncs_group { reference = (chain 'S' and resid 86 through 154) selection = chain 'W' } ncs_group { reference = (chain 'T' and (resid 19 through 136 or resid 173 through 304)) selection = (chain 'Z' and ((resid 19 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 or (resid 29 through 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 or (resid 43 through 44 and (name N or na \ me CA or name C or name O or name CB )) or resid 45 or (resid 46 through 78 and \ (name N or name CA or name C or name O or name CB )) or resid 79 or (resid 80 th \ rough 119 and (name N or name CA or name C or name O or name CB )) or resid 120 \ or (resid 121 through 123 and (name N or name CA or name C or name O or name CB \ )) or resid 124 or (resid 125 through 127 and (name N or name CA or name C or na \ me O or name CB )) or resid 128 or (resid 129 and (name N or name CA or name C o \ r name O or name CB )) or resid 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 or (resid 134 through 176 an \ d (name N or name CA or name C or name O or name CB )) or (resid 177 through 208 \ and (name N or name CA or name C or name O or name CB )) or resid 209 or (resid \ 210 through 213 and (name N or name CA or name C or name O or name CB )) or res \ id 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 or (resid 217 through 225 and (name N or name CA or name C or name O \ or name CB )) or resid 226 or (resid 227 through 231 and (name N or name CA or n \ ame C or name O or name CB )) or resid 232 or (resid 233 through 251 and (name N \ or name CA or name C or name O or name CB )) or resid 252 or (resid 253 through \ 256 and (name N or name CA or name C or name O or name CB )) or resid 257 or (r \ esid 258 through 277 and (name N or name CA or name C or name O or name CB )) or \ resid 278 or (resid 279 through 283 and (name N or name CA or name C or name O \ or name CB )) or resid 284 or (resid 285 through 304 and (name N or name CA or n \ ame C or name O or name CB )))) } ncs_group { reference = (chain 'U' and resid 8 through 158) selection = (chain 'V' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'X' and resid 8 through 158) selection = (chain 'Y' and ((resid 8 through 140 and (name N or name CA or name C or name O \ or name CB )) or (resid 141 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 or (resid 149 through 158 and (name N or name CA o \ r name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.860 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.003 0.062 39961 Z= 0.163 Angle : 0.588 10.265 54301 Z= 0.326 Chirality : 0.045 0.287 6439 Planarity : 0.005 0.061 7149 Dihedral : 13.739 165.359 14401 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.03 % Allowed : 0.32 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.11), residues: 5299 helix: 1.18 (0.09), residues: 2840 sheet: -0.69 (0.21), residues: 595 loop : -0.92 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 228 TYR 0.011 0.001 TYR A 358 PHE 0.033 0.001 PHE R 60 TRP 0.008 0.001 TRP C 471 HIS 0.004 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00325 (39961) covalent geometry : angle 0.58800 (54301) hydrogen bonds : bond 0.12835 ( 2409) hydrogen bonds : angle 5.44656 ( 7053) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 771 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 VAL cc_start: 0.8908 (p) cc_final: 0.8653 (p) REVERT: B 74 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 94 MET cc_start: 0.9279 (ttp) cc_final: 0.9005 (ttp) REVERT: B 403 GLN cc_start: 0.7942 (mt0) cc_final: 0.7715 (mm-40) REVERT: B 422 LYS cc_start: 0.8530 (tttm) cc_final: 0.7901 (mppt) REVERT: D 51 ASN cc_start: 0.8859 (p0) cc_final: 0.8521 (p0) REVERT: E 1 MET cc_start: 0.6128 (mpp) cc_final: 0.5461 (ttm) REVERT: E 337 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8361 (mm-30) REVERT: F 22 ASP cc_start: 0.8487 (p0) cc_final: 0.8097 (p0) REVERT: F 23 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8478 (mt-10) REVERT: F 126 GLN cc_start: 0.8793 (tt0) cc_final: 0.8476 (tm-30) REVERT: F 312 ASP cc_start: 0.8906 (t0) cc_final: 0.8651 (t0) REVERT: F 355 ASP cc_start: 0.8569 (t70) cc_final: 0.8205 (t0) REVERT: G 32 MET cc_start: 0.9025 (ttp) cc_final: 0.8752 (ttt) REVERT: G 50 ARG cc_start: 0.8062 (tmt170) cc_final: 0.7825 (tpt-90) REVERT: G 127 ASP cc_start: 0.8940 (m-30) cc_final: 0.8709 (m-30) REVERT: G 195 GLU cc_start: 0.7438 (tp30) cc_final: 0.6896 (tp30) REVERT: G 245 MET cc_start: 0.9230 (ttp) cc_final: 0.9002 (ttt) REVERT: R 21 MET cc_start: 0.7105 (tpt) cc_final: 0.6758 (tpp) REVERT: R 41 MET cc_start: 0.7582 (tpp) cc_final: 0.6967 (mmt) REVERT: R 48 GLU cc_start: 0.8595 (tt0) cc_final: 0.8054 (tt0) REVERT: R 70 LEU cc_start: 0.8636 (tp) cc_final: 0.8357 (tp) REVERT: R 125 ARG cc_start: 0.8574 (tpp80) cc_final: 0.8175 (mmm-85) REVERT: S 111 GLN cc_start: 0.7136 (pt0) cc_final: 0.6830 (pt0) REVERT: S 125 THR cc_start: 0.8792 (m) cc_final: 0.8429 (p) REVERT: S 148 SER cc_start: 0.8591 (t) cc_final: 0.8312 (t) REVERT: V 35 ASN cc_start: 0.8915 (m110) cc_final: 0.8698 (m110) REVERT: V 78 LYS cc_start: 0.9037 (tttp) cc_final: 0.8713 (ttpt) REVERT: V 108 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8114 (mp0) REVERT: V 121 LEU cc_start: 0.8531 (mm) cc_final: 0.8190 (pp) REVERT: V 138 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7168 (tpt-90) REVERT: W 98 SER cc_start: 0.8307 (t) cc_final: 0.8092 (p) REVERT: W 104 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.8009 (mtp-110) REVERT: W 109 LEU cc_start: 0.8373 (mt) cc_final: 0.8077 (mt) REVERT: W 136 ASP cc_start: 0.8397 (m-30) cc_final: 0.8080 (m-30) REVERT: W 137 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8207 (mm-40) REVERT: W 152 ARG cc_start: 0.4158 (mtp-110) cc_final: 0.2509 (mpt180) REVERT: H 66 ILE cc_start: 0.3552 (tt) cc_final: 0.3280 (tt) REVERT: J 5 ASN cc_start: 0.6419 (p0) cc_final: 0.6125 (p0) REVERT: J 29 SER cc_start: 0.7683 (t) cc_final: 0.7316 (t) REVERT: K 29 SER cc_start: 0.7528 (t) cc_final: 0.7323 (p) REVERT: K 37 ARG cc_start: 0.8520 (mpt-90) cc_final: 0.8186 (mpt90) REVERT: K 38 ASN cc_start: 0.8294 (t0) cc_final: 0.8091 (t0) REVERT: L 32 VAL cc_start: 0.8559 (t) cc_final: 0.8335 (p) REVERT: L 48 TYR cc_start: 0.7035 (m-80) cc_final: 0.6074 (m-80) REVERT: M 55 PHE cc_start: 0.7063 (m-80) cc_final: 0.6789 (m-10) REVERT: M 70 ILE cc_start: 0.6652 (mt) cc_final: 0.6310 (pt) REVERT: N 1 MET cc_start: 0.3728 (mtt) cc_final: 0.3020 (mmm) REVERT: N 29 SER cc_start: 0.7688 (t) cc_final: 0.7140 (p) REVERT: O 1 MET cc_start: 0.3836 (tpp) cc_final: 0.3099 (tpt) REVERT: P 1 MET cc_start: 0.4462 (mtt) cc_final: 0.3924 (tpp) REVERT: P 44 ARG cc_start: 0.5146 (tpt170) cc_final: 0.4742 (mmm-85) REVERT: P 51 ILE cc_start: 0.7231 (mt) cc_final: 0.6979 (mm) REVERT: Z 122 TRP cc_start: 0.8059 (m-10) cc_final: 0.7496 (m100) REVERT: Z 221 PHE cc_start: 0.7426 (m-80) cc_final: 0.6772 (t80) REVERT: Z 239 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8448 (pt0) REVERT: Z 276 PHE cc_start: 0.7485 (m-80) cc_final: 0.7223 (m-80) outliers start: 1 outliers final: 6 residues processed: 772 average time/residue: 0.7225 time to fit residues: 677.7253 Evaluate side-chains 493 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 487 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain L residue 35 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN B 309 HIS B 424 GLN C 207 GLN C 432 GLN D 253 ASN D 442 ASN E 128 GLN E 164 GLN E 169 ASN E 253 ASN F 174 GLN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN W 141 ASN ** J 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.138087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.084762 restraints weight = 68920.952| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.21 r_work: 0.3003 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 39961 Z= 0.254 Angle : 0.633 10.003 54301 Z= 0.329 Chirality : 0.046 0.283 6439 Planarity : 0.005 0.060 7149 Dihedral : 6.516 161.125 5899 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.60 % Allowed : 11.63 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.12), residues: 5299 helix: 1.41 (0.10), residues: 2876 sheet: -0.75 (0.21), residues: 629 loop : -0.82 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 42 TYR 0.030 0.002 TYR K 48 PHE 0.019 0.001 PHE Z 282 TRP 0.005 0.001 TRP Z 208 HIS 0.009 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00591 (39961) covalent geometry : angle 0.63310 (54301) hydrogen bonds : bond 0.04832 ( 2409) hydrogen bonds : angle 4.33021 ( 7053) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 516 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7843 (mmm-85) REVERT: A 497 ARG cc_start: 0.8657 (mmm160) cc_final: 0.7086 (tpp-160) REVERT: B 74 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 225 MET cc_start: 0.9578 (tpt) cc_final: 0.9263 (tpt) REVERT: B 403 GLN cc_start: 0.8010 (mt0) cc_final: 0.7712 (mm-40) REVERT: B 422 LYS cc_start: 0.8579 (tttm) cc_final: 0.8056 (tppp) REVERT: C 25 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7437 (tpp-160) REVERT: C 226 GLU cc_start: 0.8860 (pt0) cc_final: 0.8647 (pt0) REVERT: C 237 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: C 262 MET cc_start: 0.9168 (mmm) cc_final: 0.8953 (mmm) REVERT: D 51 ASN cc_start: 0.8921 (p0) cc_final: 0.8654 (p0) REVERT: E 1 MET cc_start: 0.6602 (mpp) cc_final: 0.5710 (ttm) REVERT: E 22 ASP cc_start: 0.8507 (m-30) cc_final: 0.8262 (p0) REVERT: E 192 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: E 253 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8486 (t0) REVERT: E 337 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8147 (mm-30) REVERT: E 395 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: F 22 ASP cc_start: 0.8530 (p0) cc_final: 0.8150 (p0) REVERT: F 23 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8691 (mt-10) REVERT: F 126 GLN cc_start: 0.9128 (tt0) cc_final: 0.8669 (tm-30) REVERT: F 312 ASP cc_start: 0.8977 (t0) cc_final: 0.8665 (t0) REVERT: F 355 ASP cc_start: 0.8656 (t70) cc_final: 0.8222 (t0) REVERT: G 32 MET cc_start: 0.9018 (ttp) cc_final: 0.8766 (ttt) REVERT: G 50 ARG cc_start: 0.8363 (tmt170) cc_final: 0.7911 (tpt-90) REVERT: G 71 GLU cc_start: 0.8662 (tt0) cc_final: 0.8002 (pp20) REVERT: G 195 GLU cc_start: 0.7641 (tp30) cc_final: 0.7235 (mm-30) REVERT: G 245 MET cc_start: 0.9229 (ttp) cc_final: 0.9025 (ttt) REVERT: R 41 MET cc_start: 0.7476 (tpp) cc_final: 0.7158 (mmt) REVERT: R 42 THR cc_start: 0.7985 (m) cc_final: 0.7751 (m) REVERT: R 48 GLU cc_start: 0.8838 (tt0) cc_final: 0.8613 (tt0) REVERT: R 112 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7974 (mpp) REVERT: R 116 GLU cc_start: 0.8064 (tp30) cc_final: 0.7837 (tp30) REVERT: S 125 THR cc_start: 0.8768 (m) cc_final: 0.8538 (p) REVERT: Y 34 MET cc_start: 0.8900 (mmp) cc_final: 0.8331 (ptp) REVERT: Y 120 MET cc_start: 0.8262 (tpp) cc_final: 0.7896 (tpp) REVERT: V 78 LYS cc_start: 0.8960 (tttp) cc_final: 0.8710 (ttpt) REVERT: V 121 LEU cc_start: 0.8640 (mm) cc_final: 0.8050 (pp) REVERT: V 138 ARG cc_start: 0.7860 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: W 93 SER cc_start: 0.8570 (m) cc_final: 0.8090 (p) REVERT: W 136 ASP cc_start: 0.8364 (m-30) cc_final: 0.8065 (m-30) REVERT: W 137 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8194 (mm-40) REVERT: W 152 ARG cc_start: 0.4233 (mtp-110) cc_final: 0.2475 (mpt180) REVERT: H 66 ILE cc_start: 0.3407 (tt) cc_final: 0.3165 (tt) REVERT: I 51 ILE cc_start: 0.7753 (tp) cc_final: 0.7481 (pp) REVERT: I 55 PHE cc_start: 0.7878 (m-80) cc_final: 0.7127 (t80) REVERT: J 5 ASN cc_start: 0.6475 (p0) cc_final: 0.6210 (p0) REVERT: J 49 MET cc_start: 0.5128 (OUTLIER) cc_final: 0.4769 (tpt) REVERT: K 24 ILE cc_start: 0.7654 (pt) cc_final: 0.7424 (pp) REVERT: K 37 ARG cc_start: 0.8340 (mpt-90) cc_final: 0.8083 (mpt90) REVERT: K 38 ASN cc_start: 0.8491 (t0) cc_final: 0.8260 (t0) REVERT: K 49 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6733 (ttm) REVERT: K 53 ILE cc_start: 0.8047 (mt) cc_final: 0.7805 (tp) REVERT: L 42 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6267 (tt0) REVERT: L 48 TYR cc_start: 0.7008 (m-80) cc_final: 0.5971 (m-80) REVERT: L 49 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6899 (ttt) REVERT: M 70 ILE cc_start: 0.6667 (mt) cc_final: 0.6374 (pt) REVERT: N 1 MET cc_start: 0.3354 (mtt) cc_final: 0.3111 (ttm) REVERT: N 29 SER cc_start: 0.7357 (t) cc_final: 0.7108 (p) REVERT: N 59 LEU cc_start: 0.7617 (mp) cc_final: 0.7352 (tp) REVERT: O 1 MET cc_start: 0.3870 (tpp) cc_final: 0.2624 (tpt) REVERT: P 44 ARG cc_start: 0.5176 (tpt170) cc_final: 0.4762 (mmm-85) REVERT: Z 22 ARG cc_start: 0.5044 (tmt170) cc_final: 0.4434 (tmm160) REVERT: Z 92 TYR cc_start: 0.7827 (t80) cc_final: 0.7136 (t80) REVERT: Z 96 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (ptp-170) REVERT: Z 122 TRP cc_start: 0.7801 (m-10) cc_final: 0.7192 (m100) REVERT: Z 217 TYR cc_start: 0.6045 (t80) cc_final: 0.5044 (t80) REVERT: Z 221 PHE cc_start: 0.7578 (m-80) cc_final: 0.6845 (t80) outliers start: 99 outliers final: 35 residues processed: 567 average time/residue: 0.6975 time to fit residues: 491.4420 Evaluate side-chains 513 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 468 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 388 ARG Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 285 MET Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 72 HIS Chi-restraints excluded: chain R residue 112 MET Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 144 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain N residue 18 ILE Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 229 optimal weight: 0.1980 chunk 110 optimal weight: 0.0670 chunk 283 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 341 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 513 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 chunk 503 optimal weight: 20.0000 chunk 298 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 457 ASN B 287 GLN B 309 HIS C 432 GLN D 253 ASN E 253 ASN F 92 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 111 GLN W 141 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.140289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087645 restraints weight = 68756.117| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.19 r_work: 0.3054 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 39961 Z= 0.129 Angle : 0.564 11.113 54301 Z= 0.290 Chirality : 0.043 0.239 6439 Planarity : 0.004 0.060 7149 Dihedral : 6.120 164.885 5891 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.47 % Allowed : 13.44 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.12), residues: 5299 helix: 1.58 (0.10), residues: 2875 sheet: -0.71 (0.21), residues: 639 loop : -0.74 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 178 TYR 0.019 0.001 TYR K 48 PHE 0.033 0.001 PHE Z 282 TRP 0.005 0.001 TRP A 471 HIS 0.011 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00289 (39961) covalent geometry : angle 0.56381 (54301) hydrogen bonds : bond 0.04240 ( 2409) hydrogen bonds : angle 4.10858 ( 7053) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 510 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8769 (m-30) cc_final: 0.8388 (m-30) REVERT: A 459 TYR cc_start: 0.8125 (m-80) cc_final: 0.7873 (m-80) REVERT: B 74 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8218 (mt-10) REVERT: B 179 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8004 (tp40) REVERT: B 225 MET cc_start: 0.9471 (tpt) cc_final: 0.9235 (tpt) REVERT: B 403 GLN cc_start: 0.7966 (mt0) cc_final: 0.7685 (mm-40) REVERT: B 422 LYS cc_start: 0.8548 (tttm) cc_final: 0.8062 (tppp) REVERT: C 25 ARG cc_start: 0.7860 (tpp-160) cc_final: 0.7421 (tpp-160) REVERT: C 221 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8332 (ptt-90) REVERT: D 51 ASN cc_start: 0.8870 (p0) cc_final: 0.8617 (p0) REVERT: D 253 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7650 (t0) REVERT: D 450 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7204 (pp20) REVERT: E 1 MET cc_start: 0.6571 (mpp) cc_final: 0.5652 (ttm) REVERT: E 101 MET cc_start: 0.8962 (mpp) cc_final: 0.8740 (mpt) REVERT: E 337 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8154 (mm-30) REVERT: E 395 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: F 22 ASP cc_start: 0.8535 (p0) cc_final: 0.8115 (p0) REVERT: F 23 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8611 (mt-10) REVERT: F 126 GLN cc_start: 0.9064 (tt0) cc_final: 0.8652 (tm-30) REVERT: F 312 ASP cc_start: 0.8855 (t0) cc_final: 0.8551 (t0) REVERT: F 355 ASP cc_start: 0.8622 (t70) cc_final: 0.8255 (t0) REVERT: F 435 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8081 (tt0) REVERT: G 32 MET cc_start: 0.9038 (ttp) cc_final: 0.8831 (ttt) REVERT: G 50 ARG cc_start: 0.8352 (tmt170) cc_final: 0.7917 (tpt-90) REVERT: G 71 GLU cc_start: 0.8676 (tt0) cc_final: 0.8122 (pp20) REVERT: G 195 GLU cc_start: 0.7555 (tp30) cc_final: 0.7265 (mm-30) REVERT: R 21 MET cc_start: 0.7160 (tpt) cc_final: 0.6857 (tpp) REVERT: R 48 GLU cc_start: 0.8819 (tt0) cc_final: 0.8608 (tt0) REVERT: R 112 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7987 (mpp) REVERT: R 116 GLU cc_start: 0.8064 (tp30) cc_final: 0.7857 (tp30) REVERT: S 104 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7635 (mmm-85) REVERT: S 107 ARG cc_start: 0.9224 (mtt180) cc_final: 0.8612 (mtm110) REVERT: S 125 THR cc_start: 0.8749 (m) cc_final: 0.8524 (p) REVERT: Y 31 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8298 (tmm-80) REVERT: Y 34 MET cc_start: 0.8909 (mmp) cc_final: 0.8273 (ptp) REVERT: V 34 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8247 (ptp) REVERT: V 57 GLN cc_start: 0.7955 (tp40) cc_final: 0.7734 (mm-40) REVERT: V 78 LYS cc_start: 0.8940 (tttp) cc_final: 0.8662 (ttpt) REVERT: V 112 GLN cc_start: 0.8677 (mp10) cc_final: 0.8378 (mp10) REVERT: V 128 ILE cc_start: 0.8773 (mm) cc_final: 0.8563 (mp) REVERT: V 138 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7223 (tpt-90) REVERT: W 93 SER cc_start: 0.8541 (m) cc_final: 0.8092 (p) REVERT: W 136 ASP cc_start: 0.8362 (m-30) cc_final: 0.8102 (m-30) REVERT: W 137 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8133 (mm-40) REVERT: W 152 ARG cc_start: 0.4621 (mtp-110) cc_final: 0.2769 (mpt180) REVERT: H 48 TYR cc_start: 0.6317 (m-80) cc_final: 0.6066 (m-80) REVERT: I 1 MET cc_start: 0.3698 (OUTLIER) cc_final: 0.2832 (tmt) REVERT: I 50 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: I 55 PHE cc_start: 0.7867 (m-80) cc_final: 0.7140 (t80) REVERT: J 5 ASN cc_start: 0.6319 (p0) cc_final: 0.6050 (p0) REVERT: J 33 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7476 (mm110) REVERT: J 49 MET cc_start: 0.5551 (tpp) cc_final: 0.5341 (tpt) REVERT: K 37 ARG cc_start: 0.8351 (mpt-90) cc_final: 0.8040 (mpt90) REVERT: L 44 ARG cc_start: 0.6591 (mtp85) cc_final: 0.5884 (mtt180) REVERT: L 48 TYR cc_start: 0.7050 (m-80) cc_final: 0.6037 (m-80) REVERT: M 70 ILE cc_start: 0.6791 (mt) cc_final: 0.6442 (pt) REVERT: N 1 MET cc_start: 0.3171 (mtt) cc_final: 0.2700 (mmm) REVERT: O 1 MET cc_start: 0.3562 (tpp) cc_final: 0.3089 (tpt) REVERT: O 9 THR cc_start: 0.4050 (OUTLIER) cc_final: 0.3821 (t) REVERT: O 37 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.6592 (mtm180) REVERT: P 44 ARG cc_start: 0.5231 (tpt170) cc_final: 0.4839 (mmm-85) REVERT: P 56 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.6988 (t) REVERT: P 70 ILE cc_start: 0.4278 (mt) cc_final: 0.4072 (mp) REVERT: Q 68 PHE cc_start: 0.6800 (m-10) cc_final: 0.6157 (m-80) REVERT: Z 22 ARG cc_start: 0.5016 (tmt170) cc_final: 0.4349 (tmm160) REVERT: Z 26 TYR cc_start: 0.6628 (t80) cc_final: 0.6122 (t80) REVERT: Z 96 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7795 (ptp-170) REVERT: Z 122 TRP cc_start: 0.7881 (m-10) cc_final: 0.7296 (m100) REVERT: Z 221 PHE cc_start: 0.7496 (m-80) cc_final: 0.6788 (t80) REVERT: Z 235 GLU cc_start: 0.8232 (pp20) cc_final: 0.7557 (pp20) REVERT: Z 264 MET cc_start: 0.7484 (mmm) cc_final: 0.7238 (ptt) REVERT: Z 282 PHE cc_start: 0.7899 (t80) cc_final: 0.7518 (t80) REVERT: Z 285 PHE cc_start: 0.8270 (t80) cc_final: 0.7982 (t80) outliers start: 94 outliers final: 34 residues processed: 556 average time/residue: 0.7003 time to fit residues: 482.4192 Evaluate side-chains 517 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 469 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 104 ARG Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 112 MET Chi-restraints excluded: chain Y residue 31 ARG Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 122 SER Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 274 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 384 optimal weight: 50.0000 chunk 27 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 512 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 439 optimal weight: 9.9990 chunk 389 optimal weight: 50.0000 chunk 372 optimal weight: 4.9990 chunk 485 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN B 287 GLN B 309 HIS C 432 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN ** F 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS Y 38 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082470 restraints weight = 68945.663| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.17 r_work: 0.2962 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 39961 Z= 0.287 Angle : 0.648 12.914 54301 Z= 0.334 Chirality : 0.047 0.248 6439 Planarity : 0.005 0.059 7149 Dihedral : 6.381 159.332 5891 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.34 % Allowed : 15.00 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.12), residues: 5299 helix: 1.51 (0.10), residues: 2863 sheet: -0.89 (0.21), residues: 640 loop : -0.76 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 41 TYR 0.016 0.002 TYR I 48 PHE 0.025 0.002 PHE Z 282 TRP 0.007 0.001 TRP Z 122 HIS 0.009 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00678 (39961) covalent geometry : angle 0.64788 (54301) hydrogen bonds : bond 0.04566 ( 2409) hydrogen bonds : angle 4.18620 ( 7053) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 477 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8793 (m-30) cc_final: 0.8456 (m-30) REVERT: A 497 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8352 (tpp80) REVERT: B 74 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 179 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8212 (tp40) REVERT: B 403 GLN cc_start: 0.8037 (mt0) cc_final: 0.7679 (mm-40) REVERT: B 422 LYS cc_start: 0.8579 (tttm) cc_final: 0.8124 (tppp) REVERT: C 25 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7452 (tpp-160) REVERT: C 221 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8262 (ptt-90) REVERT: D 51 ASN cc_start: 0.8957 (p0) cc_final: 0.8709 (p0) REVERT: D 192 ASP cc_start: 0.7329 (m-30) cc_final: 0.6883 (m-30) REVERT: D 450 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7451 (pp20) REVERT: D 455 MET cc_start: 0.8595 (mmt) cc_final: 0.8053 (mmt) REVERT: E 1 MET cc_start: 0.6734 (mpp) cc_final: 0.5757 (ttm) REVERT: E 192 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: E 337 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8216 (mm-30) REVERT: E 395 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: F 22 ASP cc_start: 0.8527 (p0) cc_final: 0.8122 (p0) REVERT: F 23 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8719 (mt-10) REVERT: F 126 GLN cc_start: 0.9137 (tt0) cc_final: 0.8709 (tm-30) REVERT: F 204 GLU cc_start: 0.7433 (pp20) cc_final: 0.7035 (pp20) REVERT: F 312 ASP cc_start: 0.8989 (t0) cc_final: 0.8736 (t0) REVERT: F 355 ASP cc_start: 0.8653 (t70) cc_final: 0.8271 (t0) REVERT: G 32 MET cc_start: 0.9032 (ttp) cc_final: 0.8797 (ttt) REVERT: G 50 ARG cc_start: 0.8382 (tmt170) cc_final: 0.8043 (tpt-90) REVERT: G 71 GLU cc_start: 0.8728 (tt0) cc_final: 0.8150 (pp20) REVERT: R 21 MET cc_start: 0.7214 (tpt) cc_final: 0.6873 (tpp) REVERT: R 36 ARG cc_start: 0.7356 (tpm170) cc_final: 0.6842 (mtp85) REVERT: R 48 GLU cc_start: 0.8887 (tt0) cc_final: 0.8636 (tt0) REVERT: R 116 GLU cc_start: 0.8260 (tp30) cc_final: 0.7922 (tp30) REVERT: S 104 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7519 (mmm-85) REVERT: S 107 ARG cc_start: 0.9254 (mtt180) cc_final: 0.8599 (mtm110) REVERT: S 125 THR cc_start: 0.8808 (m) cc_final: 0.8591 (p) REVERT: V 34 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8231 (ptp) REVERT: V 57 GLN cc_start: 0.8026 (tp40) cc_final: 0.7436 (tt0) REVERT: V 78 LYS cc_start: 0.9000 (tttp) cc_final: 0.8726 (ttpt) REVERT: V 112 GLN cc_start: 0.8493 (mp10) cc_final: 0.8106 (mp10) REVERT: V 128 ILE cc_start: 0.8769 (mm) cc_final: 0.8537 (mp) REVERT: V 138 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: W 136 ASP cc_start: 0.8429 (m-30) cc_final: 0.8104 (m-30) REVERT: W 137 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8233 (mm-40) REVERT: W 152 ARG cc_start: 0.5252 (mtp-110) cc_final: 0.3131 (mpt180) REVERT: H 66 ILE cc_start: 0.3440 (tt) cc_final: 0.3163 (tt) REVERT: I 1 MET cc_start: 0.3676 (OUTLIER) cc_final: 0.3374 (tmt) REVERT: I 35 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7137 (tt) REVERT: I 55 PHE cc_start: 0.7933 (m-80) cc_final: 0.7250 (t80) REVERT: J 5 ASN cc_start: 0.6385 (p0) cc_final: 0.6119 (p0) REVERT: J 33 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7638 (mm110) REVERT: K 33 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7259 (mm110) REVERT: K 35 ILE cc_start: 0.8666 (mp) cc_final: 0.8393 (mm) REVERT: K 37 ARG cc_start: 0.8394 (mpt-90) cc_final: 0.8102 (mpt90) REVERT: K 70 ILE cc_start: 0.4229 (tt) cc_final: 0.4004 (tt) REVERT: L 44 ARG cc_start: 0.6638 (mtp85) cc_final: 0.5784 (mtt180) REVERT: L 48 TYR cc_start: 0.7125 (m-80) cc_final: 0.6024 (m-80) REVERT: N 1 MET cc_start: 0.3448 (mtt) cc_final: 0.3208 (ttm) REVERT: O 1 MET cc_start: 0.3708 (tpp) cc_final: 0.3124 (tpt) REVERT: O 9 THR cc_start: 0.3989 (OUTLIER) cc_final: 0.3768 (t) REVERT: P 1 MET cc_start: 0.5675 (tpp) cc_final: 0.4550 (mmt) REVERT: P 44 ARG cc_start: 0.5210 (tpt170) cc_final: 0.4769 (mmm-85) REVERT: Q 68 PHE cc_start: 0.6849 (m-10) cc_final: 0.6250 (m-80) REVERT: Z 22 ARG cc_start: 0.5083 (tmt170) cc_final: 0.4457 (tmm160) REVERT: Z 26 TYR cc_start: 0.6706 (t80) cc_final: 0.6213 (t80) REVERT: Z 96 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7766 (ptp-170) REVERT: Z 122 TRP cc_start: 0.7857 (m-10) cc_final: 0.7224 (m100) REVERT: Z 221 PHE cc_start: 0.7496 (m-80) cc_final: 0.6796 (t80) REVERT: Z 228 MET cc_start: 0.4498 (OUTLIER) cc_final: 0.3907 (tpt) REVERT: Z 282 PHE cc_start: 0.7867 (t80) cc_final: 0.7540 (t80) outliers start: 127 outliers final: 58 residues processed: 548 average time/residue: 0.7128 time to fit residues: 484.1113 Evaluate side-chains 514 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 445 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 80 THR Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 133 THR Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain W residue 125 THR Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 118 LEU Chi-restraints excluded: chain Z residue 228 MET Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 54 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 515 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 301 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 431 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 309 HIS C 432 GLN D 46 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 442 ASN E 253 ASN F 195 HIS S 117 HIS W 137 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085447 restraints weight = 68104.260| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.18 r_work: 0.3023 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39961 Z= 0.140 Angle : 0.577 13.405 54301 Z= 0.296 Chirality : 0.044 0.255 6439 Planarity : 0.005 0.121 7149 Dihedral : 6.474 166.191 5891 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.97 % Allowed : 16.81 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.12), residues: 5299 helix: 1.66 (0.10), residues: 2884 sheet: -0.90 (0.21), residues: 633 loop : -0.72 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 41 TYR 0.031 0.001 TYR H 48 PHE 0.019 0.001 PHE Z 282 TRP 0.005 0.001 TRP Z 208 HIS 0.009 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00317 (39961) covalent geometry : angle 0.57676 (54301) hydrogen bonds : bond 0.04135 ( 2409) hydrogen bonds : angle 4.04992 ( 7053) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 495 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8748 (m-30) cc_final: 0.8400 (m-30) REVERT: A 497 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8392 (tpp80) REVERT: B 74 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 179 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8078 (tp40) REVERT: B 225 MET cc_start: 0.9493 (tpt) cc_final: 0.9167 (tpt) REVERT: B 403 GLN cc_start: 0.7946 (mt0) cc_final: 0.7664 (mm-40) REVERT: B 422 LYS cc_start: 0.8608 (tttm) cc_final: 0.8181 (tppp) REVERT: C 221 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8315 (ptt-90) REVERT: D 192 ASP cc_start: 0.6872 (m-30) cc_final: 0.6245 (m-30) REVERT: E 1 MET cc_start: 0.6686 (mpp) cc_final: 0.5662 (ttm) REVERT: E 101 MET cc_start: 0.8969 (mpp) cc_final: 0.8733 (mpt) REVERT: E 189 GLU cc_start: 0.8443 (tp30) cc_final: 0.8232 (tp30) REVERT: E 221 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: E 253 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8392 (t0) REVERT: E 337 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 395 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: F 22 ASP cc_start: 0.8519 (p0) cc_final: 0.8166 (p0) REVERT: F 23 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8652 (mt-10) REVERT: F 126 GLN cc_start: 0.9118 (tt0) cc_final: 0.8703 (tm-30) REVERT: F 312 ASP cc_start: 0.8896 (t0) cc_final: 0.8591 (t0) REVERT: F 355 ASP cc_start: 0.8639 (t70) cc_final: 0.8258 (t0) REVERT: G 32 MET cc_start: 0.9016 (ttp) cc_final: 0.8795 (ttt) REVERT: G 50 ARG cc_start: 0.8356 (tmt170) cc_final: 0.7958 (tpt-90) REVERT: G 71 GLU cc_start: 0.8773 (tt0) cc_final: 0.8137 (pp20) REVERT: R 21 MET cc_start: 0.7146 (tpt) cc_final: 0.6867 (tpp) REVERT: R 48 GLU cc_start: 0.8834 (tt0) cc_final: 0.8250 (tt0) REVERT: R 60 PHE cc_start: 0.6242 (OUTLIER) cc_final: 0.5041 (t80) REVERT: R 116 GLU cc_start: 0.8123 (tp30) cc_final: 0.7806 (tp30) REVERT: S 125 THR cc_start: 0.8747 (m) cc_final: 0.8542 (p) REVERT: V 57 GLN cc_start: 0.7997 (tp40) cc_final: 0.7455 (tt0) REVERT: V 78 LYS cc_start: 0.8956 (tttp) cc_final: 0.8691 (ttpt) REVERT: V 112 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: V 128 ILE cc_start: 0.8749 (mm) cc_final: 0.8534 (mp) REVERT: V 138 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7391 (tpp-160) REVERT: W 136 ASP cc_start: 0.8403 (m-30) cc_final: 0.8092 (m-30) REVERT: W 137 GLN cc_start: 0.8602 (mm110) cc_final: 0.8202 (mm-40) REVERT: W 152 ARG cc_start: 0.5410 (mtp-110) cc_final: 0.3312 (mpt180) REVERT: H 50 PHE cc_start: 0.6403 (m-80) cc_final: 0.6182 (m-80) REVERT: H 66 ILE cc_start: 0.3304 (tt) cc_final: 0.3017 (tt) REVERT: I 1 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.3101 (tmt) REVERT: I 35 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.7225 (tt) REVERT: I 50 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: I 55 PHE cc_start: 0.7886 (m-80) cc_final: 0.7186 (t80) REVERT: J 5 ASN cc_start: 0.6281 (p0) cc_final: 0.6004 (p0) REVERT: J 33 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7706 (mm110) REVERT: J 37 ARG cc_start: 0.8020 (mmp80) cc_final: 0.7809 (mmp80) REVERT: J 46 VAL cc_start: 0.7518 (t) cc_final: 0.7280 (m) REVERT: K 33 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7176 (mm110) REVERT: K 35 ILE cc_start: 0.8681 (mt) cc_final: 0.8434 (mm) REVERT: K 37 ARG cc_start: 0.8386 (mpt-90) cc_final: 0.8017 (mpt90) REVERT: L 44 ARG cc_start: 0.6604 (mtp85) cc_final: 0.5826 (mtt180) REVERT: L 48 TYR cc_start: 0.7234 (m-80) cc_final: 0.6133 (m-80) REVERT: N 1 MET cc_start: 0.3398 (mtt) cc_final: 0.3168 (ttm) REVERT: N 5 ASN cc_start: 0.7097 (p0) cc_final: 0.6800 (p0) REVERT: N 29 SER cc_start: 0.6985 (OUTLIER) cc_final: 0.6745 (p) REVERT: O 1 MET cc_start: 0.3638 (tpp) cc_final: 0.3069 (tpt) REVERT: O 9 THR cc_start: 0.4070 (OUTLIER) cc_final: 0.3845 (t) REVERT: P 1 MET cc_start: 0.5577 (tpp) cc_final: 0.4429 (mmt) REVERT: P 44 ARG cc_start: 0.5281 (tpt170) cc_final: 0.4820 (mmm-85) REVERT: P 56 THR cc_start: 0.7428 (OUTLIER) cc_final: 0.7068 (t) REVERT: Q 68 PHE cc_start: 0.6776 (m-10) cc_final: 0.6185 (m-80) REVERT: Z 75 MET cc_start: 0.7919 (tpt) cc_final: 0.7612 (mmm) REVERT: Z 85 GLU cc_start: 0.7486 (tt0) cc_final: 0.6837 (tp30) REVERT: Z 92 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7045 (t80) REVERT: Z 96 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7789 (ptp-170) REVERT: Z 122 TRP cc_start: 0.7928 (m-10) cc_final: 0.7311 (m100) REVERT: Z 221 PHE cc_start: 0.7471 (m-80) cc_final: 0.6780 (t80) REVERT: Z 228 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4075 (tpt) REVERT: Z 235 GLU cc_start: 0.8363 (pp20) cc_final: 0.7761 (pp20) REVERT: Z 282 PHE cc_start: 0.7885 (t80) cc_final: 0.7470 (t80) outliers start: 113 outliers final: 46 residues processed: 561 average time/residue: 0.6686 time to fit residues: 470.7063 Evaluate side-chains 537 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 475 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 112 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 92 TYR Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 207 TYR Chi-restraints excluded: chain Z residue 228 MET Chi-restraints excluded: chain Z residue 260 LEU Chi-restraints excluded: chain Z residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 270 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 467 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 254 optimal weight: 0.0010 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 432 GLN D 51 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 442 ASN E 205 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.084611 restraints weight = 68499.669| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.18 r_work: 0.3010 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39961 Z= 0.170 Angle : 0.594 13.076 54301 Z= 0.303 Chirality : 0.044 0.265 6439 Planarity : 0.004 0.058 7149 Dihedral : 6.501 177.190 5891 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.68 % Allowed : 18.31 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.12), residues: 5299 helix: 1.67 (0.10), residues: 2891 sheet: -0.88 (0.21), residues: 639 loop : -0.67 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 41 TYR 0.022 0.001 TYR H 48 PHE 0.016 0.001 PHE Z 282 TRP 0.007 0.001 TRP Z 208 HIS 0.017 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00397 (39961) covalent geometry : angle 0.59369 (54301) hydrogen bonds : bond 0.04145 ( 2409) hydrogen bonds : angle 4.03288 ( 7053) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 473 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8400 (tpp80) REVERT: B 74 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8380 (mt-10) REVERT: B 179 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: B 225 MET cc_start: 0.9524 (tpt) cc_final: 0.9156 (tpt) REVERT: B 403 GLN cc_start: 0.7978 (mt0) cc_final: 0.7626 (mm-40) REVERT: B 422 LYS cc_start: 0.8601 (tttm) cc_final: 0.8195 (tppp) REVERT: C 25 ARG cc_start: 0.7688 (tpp-160) cc_final: 0.7244 (tpp-160) REVERT: C 221 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8272 (ptt-90) REVERT: D 192 ASP cc_start: 0.6950 (m-30) cc_final: 0.6306 (m-30) REVERT: D 253 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (t0) REVERT: D 450 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: D 467 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: E 1 MET cc_start: 0.6698 (mpp) cc_final: 0.5677 (ttm) REVERT: E 189 GLU cc_start: 0.8417 (tp30) cc_final: 0.8179 (tp30) REVERT: E 221 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8772 (mt-10) REVERT: E 337 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8193 (mm-30) REVERT: E 395 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: F 22 ASP cc_start: 0.8523 (p0) cc_final: 0.8172 (p0) REVERT: F 23 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8671 (mt-10) REVERT: F 92 ASN cc_start: 0.8595 (m-40) cc_final: 0.8263 (m110) REVERT: F 126 GLN cc_start: 0.9092 (tt0) cc_final: 0.8721 (tm-30) REVERT: F 312 ASP cc_start: 0.8839 (t0) cc_final: 0.8520 (t0) REVERT: F 355 ASP cc_start: 0.8621 (t70) cc_final: 0.8233 (t0) REVERT: F 431 LYS cc_start: 0.8743 (tttt) cc_final: 0.8415 (tptp) REVERT: G 50 ARG cc_start: 0.8307 (tmt170) cc_final: 0.7921 (tpt-90) REVERT: G 71 GLU cc_start: 0.8779 (tt0) cc_final: 0.8226 (pp20) REVERT: G 112 MET cc_start: 0.8758 (ttp) cc_final: 0.8549 (ttm) REVERT: R 21 MET cc_start: 0.7152 (tpt) cc_final: 0.6886 (tpp) REVERT: R 48 GLU cc_start: 0.8838 (tt0) cc_final: 0.8248 (tt0) REVERT: R 60 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5004 (t80) REVERT: S 102 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7566 (mttp) REVERT: S 125 THR cc_start: 0.8737 (m) cc_final: 0.8534 (p) REVERT: V 57 GLN cc_start: 0.7989 (tp40) cc_final: 0.7441 (tt0) REVERT: V 78 LYS cc_start: 0.8971 (tttp) cc_final: 0.8709 (ttpt) REVERT: V 112 GLN cc_start: 0.8425 (mp10) cc_final: 0.8086 (mp10) REVERT: V 128 ILE cc_start: 0.8765 (mm) cc_final: 0.8534 (mp) REVERT: V 138 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7454 (tpp-160) REVERT: W 136 ASP cc_start: 0.8411 (m-30) cc_final: 0.8079 (m-30) REVERT: W 137 GLN cc_start: 0.8625 (mm110) cc_final: 0.8218 (mm-40) REVERT: W 152 ARG cc_start: 0.5335 (mtp-110) cc_final: 0.3343 (mpt180) REVERT: H 66 ILE cc_start: 0.3396 (tt) cc_final: 0.3107 (tt) REVERT: I 1 MET cc_start: 0.3878 (OUTLIER) cc_final: 0.3362 (tmt) REVERT: I 50 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: I 55 PHE cc_start: 0.7884 (m-80) cc_final: 0.7200 (t80) REVERT: J 5 ASN cc_start: 0.6284 (p0) cc_final: 0.6001 (p0) REVERT: J 46 VAL cc_start: 0.7565 (t) cc_final: 0.7356 (m) REVERT: K 33 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7356 (mm110) REVERT: K 35 ILE cc_start: 0.8776 (mt) cc_final: 0.8545 (mm) REVERT: K 37 ARG cc_start: 0.8403 (mpt-90) cc_final: 0.8098 (mpt90) REVERT: K 49 MET cc_start: 0.6970 (ttp) cc_final: 0.6674 (ttm) REVERT: K 70 ILE cc_start: 0.4391 (tt) cc_final: 0.3862 (mt) REVERT: L 44 ARG cc_start: 0.6679 (mtp85) cc_final: 0.5903 (mtt180) REVERT: L 48 TYR cc_start: 0.7345 (m-80) cc_final: 0.6273 (m-80) REVERT: N 5 ASN cc_start: 0.7132 (p0) cc_final: 0.6873 (p0) REVERT: N 29 SER cc_start: 0.7072 (OUTLIER) cc_final: 0.6860 (p) REVERT: O 1 MET cc_start: 0.3596 (tpp) cc_final: 0.3037 (tpt) REVERT: O 9 THR cc_start: 0.4179 (OUTLIER) cc_final: 0.3972 (t) REVERT: P 1 MET cc_start: 0.5661 (tpp) cc_final: 0.4515 (mmt) REVERT: P 44 ARG cc_start: 0.5351 (tpt170) cc_final: 0.4983 (mmm160) REVERT: P 56 THR cc_start: 0.7391 (OUTLIER) cc_final: 0.7064 (t) REVERT: Q 53 ILE cc_start: 0.4734 (pt) cc_final: 0.4398 (pt) REVERT: Z 75 MET cc_start: 0.7899 (tpt) cc_final: 0.7647 (mmm) REVERT: Z 85 GLU cc_start: 0.7553 (tt0) cc_final: 0.6912 (tp30) REVERT: Z 92 TYR cc_start: 0.7441 (t80) cc_final: 0.7012 (t80) REVERT: Z 96 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (ptp-170) REVERT: Z 122 TRP cc_start: 0.8024 (m-10) cc_final: 0.7422 (m100) REVERT: Z 221 PHE cc_start: 0.7462 (m-80) cc_final: 0.6772 (t80) REVERT: Z 228 MET cc_start: 0.4954 (OUTLIER) cc_final: 0.4452 (tpt) REVERT: Z 282 PHE cc_start: 0.7975 (t80) cc_final: 0.7564 (t80) outliers start: 102 outliers final: 50 residues processed: 534 average time/residue: 0.6054 time to fit residues: 404.9371 Evaluate side-chains 518 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 453 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 207 TYR Chi-restraints excluded: chain Z residue 228 MET Chi-restraints excluded: chain Z residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 323 optimal weight: 0.0870 chunk 360 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 426 optimal weight: 8.9990 chunk 487 optimal weight: 0.7980 chunk 405 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 226 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 309 HIS C 432 GLN D 51 ASN D 218 GLN D 253 ASN D 442 ASN E 164 GLN E 253 ASN F 195 HIS S 117 HIS W 101 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.086332 restraints weight = 68366.897| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.17 r_work: 0.3037 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39961 Z= 0.134 Angle : 0.593 13.430 54301 Z= 0.303 Chirality : 0.044 0.361 6439 Planarity : 0.004 0.057 7149 Dihedral : 6.390 179.813 5891 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.68 % Allowed : 18.47 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.12), residues: 5299 helix: 1.73 (0.10), residues: 2863 sheet: -0.86 (0.21), residues: 629 loop : -0.66 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 41 TYR 0.022 0.001 TYR H 48 PHE 0.023 0.001 PHE L 62 TRP 0.007 0.001 TRP Z 208 HIS 0.004 0.001 HIS S 117 Details of bonding type rmsd covalent geometry : bond 0.00308 (39961) covalent geometry : angle 0.59325 (54301) hydrogen bonds : bond 0.04077 ( 2409) hydrogen bonds : angle 4.01925 ( 7053) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 492 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8856 (m-30) cc_final: 0.8625 (m-30) REVERT: A 459 TYR cc_start: 0.8209 (m-80) cc_final: 0.7994 (m-80) REVERT: A 497 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8418 (tpp80) REVERT: B 74 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 85 ASP cc_start: 0.8187 (m-30) cc_final: 0.7946 (m-30) REVERT: B 179 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7991 (tp40) REVERT: B 225 MET cc_start: 0.9496 (tpt) cc_final: 0.9170 (tpt) REVERT: B 403 GLN cc_start: 0.7908 (mt0) cc_final: 0.7570 (mm-40) REVERT: B 422 LYS cc_start: 0.8628 (tttm) cc_final: 0.8215 (tppp) REVERT: C 25 ARG cc_start: 0.7728 (tpp-160) cc_final: 0.7249 (tpp-160) REVERT: C 221 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8263 (ptt-90) REVERT: D 101 MET cc_start: 0.9076 (mpt) cc_final: 0.8818 (mpm) REVERT: D 192 ASP cc_start: 0.6820 (m-30) cc_final: 0.6078 (m-30) REVERT: D 450 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: D 467 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: E 1 MET cc_start: 0.6660 (mpp) cc_final: 0.5737 (ttm) REVERT: E 121 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: E 189 GLU cc_start: 0.8377 (tp30) cc_final: 0.8150 (tp30) REVERT: E 221 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8836 (mt-10) REVERT: E 253 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8511 (t0) REVERT: E 337 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8158 (mm-30) REVERT: E 389 MET cc_start: 0.8424 (mtm) cc_final: 0.7784 (mpp) REVERT: E 395 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7554 (pp20) REVERT: F 22 ASP cc_start: 0.8492 (p0) cc_final: 0.8141 (p0) REVERT: F 23 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8635 (mt-10) REVERT: F 92 ASN cc_start: 0.8471 (m-40) cc_final: 0.8115 (m110) REVERT: F 126 GLN cc_start: 0.9079 (tt0) cc_final: 0.8719 (tm-30) REVERT: F 204 GLU cc_start: 0.7600 (pp20) cc_final: 0.7134 (pp20) REVERT: F 312 ASP cc_start: 0.8761 (t0) cc_final: 0.8470 (t0) REVERT: F 355 ASP cc_start: 0.8620 (t70) cc_final: 0.8233 (t0) REVERT: F 431 LYS cc_start: 0.8755 (tttt) cc_final: 0.8460 (tptp) REVERT: F 467 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: G 50 ARG cc_start: 0.8328 (tmt170) cc_final: 0.7937 (tpt-90) REVERT: G 71 GLU cc_start: 0.8772 (tt0) cc_final: 0.8308 (pp20) REVERT: G 112 MET cc_start: 0.8749 (ttp) cc_final: 0.8541 (ttm) REVERT: G 245 MET cc_start: 0.9226 (ttt) cc_final: 0.9012 (ttt) REVERT: R 21 MET cc_start: 0.7158 (tpt) cc_final: 0.6908 (tpp) REVERT: R 48 GLU cc_start: 0.8859 (tt0) cc_final: 0.8261 (tt0) REVERT: R 60 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5049 (t80) REVERT: S 102 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7569 (mttp) REVERT: Y 53 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7234 (mtmp) REVERT: V 57 GLN cc_start: 0.7971 (tp40) cc_final: 0.7739 (mm-40) REVERT: V 78 LYS cc_start: 0.8960 (tttp) cc_final: 0.8715 (ttpt) REVERT: V 128 ILE cc_start: 0.8754 (mm) cc_final: 0.8524 (mp) REVERT: V 138 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.7361 (tpp-160) REVERT: W 136 ASP cc_start: 0.8441 (m-30) cc_final: 0.8120 (m-30) REVERT: W 137 GLN cc_start: 0.8676 (mm110) cc_final: 0.8296 (mm-40) REVERT: W 152 ARG cc_start: 0.5537 (mtp-110) cc_final: 0.3367 (mpt180) REVERT: H 66 ILE cc_start: 0.3352 (tt) cc_final: 0.3098 (tt) REVERT: I 1 MET cc_start: 0.4130 (OUTLIER) cc_final: 0.3638 (tmt) REVERT: I 35 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.6998 (tp) REVERT: I 50 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: I 55 PHE cc_start: 0.7866 (m-80) cc_final: 0.7197 (t80) REVERT: J 5 ASN cc_start: 0.6317 (p0) cc_final: 0.6030 (p0) REVERT: K 33 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7330 (mm110) REVERT: K 37 ARG cc_start: 0.8404 (mpt-90) cc_final: 0.8110 (mpt90) REVERT: K 70 ILE cc_start: 0.4357 (tt) cc_final: 0.4012 (mt) REVERT: L 42 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6446 (pp20) REVERT: L 44 ARG cc_start: 0.6666 (mtp85) cc_final: 0.5826 (mtt180) REVERT: L 48 TYR cc_start: 0.7342 (m-80) cc_final: 0.6261 (m-80) REVERT: N 5 ASN cc_start: 0.7087 (p0) cc_final: 0.6864 (p0) REVERT: O 1 MET cc_start: 0.3373 (tpp) cc_final: 0.3072 (tpt) REVERT: P 1 MET cc_start: 0.5577 (tpp) cc_final: 0.4466 (mmt) REVERT: P 44 ARG cc_start: 0.5294 (tpt170) cc_final: 0.4927 (mmm160) REVERT: P 56 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7299 (t) REVERT: Q 68 PHE cc_start: 0.6750 (m-80) cc_final: 0.6193 (m-80) REVERT: Z 26 TYR cc_start: 0.6762 (t80) cc_final: 0.6485 (t80) REVERT: Z 75 MET cc_start: 0.7836 (tpt) cc_final: 0.7630 (mmm) REVERT: Z 85 GLU cc_start: 0.7479 (tt0) cc_final: 0.6875 (tp30) REVERT: Z 92 TYR cc_start: 0.7479 (t80) cc_final: 0.7077 (t80) REVERT: Z 96 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (ptp-170) REVERT: Z 122 TRP cc_start: 0.8035 (m-10) cc_final: 0.7451 (m100) REVERT: Z 221 PHE cc_start: 0.7429 (m-80) cc_final: 0.6708 (t80) REVERT: Z 228 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4468 (tpt) REVERT: Z 235 GLU cc_start: 0.8327 (pp20) cc_final: 0.7900 (pp20) REVERT: Z 282 PHE cc_start: 0.7928 (t80) cc_final: 0.7507 (t80) outliers start: 102 outliers final: 51 residues processed: 554 average time/residue: 0.6158 time to fit residues: 428.6699 Evaluate side-chains 543 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 475 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain R residue 72 HIS Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 112 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 317 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 345 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 chunk 366 optimal weight: 1.9990 chunk 327 optimal weight: 9.9990 chunk 408 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 432 GLN D 51 ASN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN E 205 ASN E 253 ASN F 195 HIS S 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.082779 restraints weight = 68586.926| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.20 r_work: 0.2971 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 39961 Z= 0.260 Angle : 0.665 13.528 54301 Z= 0.339 Chirality : 0.047 0.268 6439 Planarity : 0.005 0.060 7149 Dihedral : 6.616 179.253 5891 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.05 % Allowed : 18.78 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.12), residues: 5299 helix: 1.61 (0.10), residues: 2864 sheet: -0.95 (0.21), residues: 619 loop : -0.74 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 41 TYR 0.024 0.002 TYR W 113 PHE 0.037 0.001 PHE L 62 TRP 0.010 0.001 TRP Z 122 HIS 0.005 0.001 HIS R 37 Details of bonding type rmsd covalent geometry : bond 0.00620 (39961) covalent geometry : angle 0.66513 (54301) hydrogen bonds : bond 0.04377 ( 2409) hydrogen bonds : angle 4.14189 ( 7053) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 477 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8892 (m-30) cc_final: 0.8659 (m-30) REVERT: B 74 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 85 ASP cc_start: 0.8281 (m-30) cc_final: 0.8012 (m-30) REVERT: B 179 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8164 (tp40) REVERT: B 403 GLN cc_start: 0.7998 (mt0) cc_final: 0.7676 (mm-40) REVERT: B 422 LYS cc_start: 0.8610 (tttm) cc_final: 0.8179 (tppp) REVERT: C 13 LYS cc_start: 0.8986 (tttt) cc_final: 0.8782 (mtpt) REVERT: C 25 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7404 (tpp-160) REVERT: C 221 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8280 (ptt-90) REVERT: D 101 MET cc_start: 0.9049 (mpt) cc_final: 0.8823 (mpm) REVERT: D 450 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: D 467 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: E 1 MET cc_start: 0.6727 (mpp) cc_final: 0.5643 (ttm) REVERT: E 189 GLU cc_start: 0.8435 (tp30) cc_final: 0.8219 (tp30) REVERT: E 221 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8782 (mt-10) REVERT: E 253 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8604 (t0) REVERT: E 337 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8192 (mm-30) REVERT: E 395 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: F 22 ASP cc_start: 0.8537 (p0) cc_final: 0.8170 (p0) REVERT: F 23 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8665 (mt-10) REVERT: F 126 GLN cc_start: 0.9115 (tt0) cc_final: 0.8731 (tm-30) REVERT: F 204 GLU cc_start: 0.7711 (pp20) cc_final: 0.7202 (pp20) REVERT: F 312 ASP cc_start: 0.8941 (t0) cc_final: 0.8625 (t0) REVERT: F 355 ASP cc_start: 0.8639 (t70) cc_final: 0.8223 (t0) REVERT: F 431 LYS cc_start: 0.8790 (tttt) cc_final: 0.8485 (tptp) REVERT: G 71 GLU cc_start: 0.8829 (tt0) cc_final: 0.8270 (pp20) REVERT: G 112 MET cc_start: 0.8816 (ttp) cc_final: 0.8564 (ttm) REVERT: G 245 MET cc_start: 0.9203 (ttt) cc_final: 0.8980 (ttt) REVERT: R 21 MET cc_start: 0.7207 (tpt) cc_final: 0.6933 (tpp) REVERT: R 48 GLU cc_start: 0.8897 (tt0) cc_final: 0.8304 (tt0) REVERT: R 60 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5038 (t80) REVERT: R 94 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8565 (pp30) REVERT: S 102 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7718 (mttp) REVERT: Y 34 MET cc_start: 0.8678 (mmp) cc_final: 0.8191 (mtm) REVERT: Y 120 MET cc_start: 0.8280 (tpp) cc_final: 0.7958 (tpp) REVERT: V 57 GLN cc_start: 0.8024 (tp40) cc_final: 0.7476 (tt0) REVERT: V 78 LYS cc_start: 0.8947 (tttp) cc_final: 0.8687 (ttpt) REVERT: V 128 ILE cc_start: 0.8750 (mm) cc_final: 0.8508 (mp) REVERT: V 138 ARG cc_start: 0.7817 (tpp-160) cc_final: 0.7423 (tpp-160) REVERT: W 136 ASP cc_start: 0.8453 (m-30) cc_final: 0.8120 (m-30) REVERT: W 137 GLN cc_start: 0.8654 (mm110) cc_final: 0.8236 (mm-40) REVERT: W 152 ARG cc_start: 0.5951 (mtp-110) cc_final: 0.3606 (mpt180) REVERT: H 66 ILE cc_start: 0.3366 (tt) cc_final: 0.3102 (tt) REVERT: I 35 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6975 (tp) REVERT: I 50 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: I 55 PHE cc_start: 0.7894 (m-80) cc_final: 0.7208 (t80) REVERT: J 5 ASN cc_start: 0.6440 (p0) cc_final: 0.6163 (p0) REVERT: K 33 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7350 (mm110) REVERT: K 37 ARG cc_start: 0.8439 (mpt-90) cc_final: 0.8085 (mpt90) REVERT: K 70 ILE cc_start: 0.4398 (tt) cc_final: 0.4130 (mt) REVERT: L 42 GLU cc_start: 0.6534 (tm-30) cc_final: 0.6314 (pp20) REVERT: L 44 ARG cc_start: 0.6631 (mtp85) cc_final: 0.5812 (mtt180) REVERT: L 48 TYR cc_start: 0.7353 (m-80) cc_final: 0.6192 (m-80) REVERT: N 5 ASN cc_start: 0.7141 (p0) cc_final: 0.6915 (p0) REVERT: O 1 MET cc_start: 0.3205 (tpp) cc_final: 0.2889 (tpt) REVERT: P 1 MET cc_start: 0.5778 (tpp) cc_final: 0.4858 (mmt) REVERT: P 44 ARG cc_start: 0.5424 (tpt170) cc_final: 0.5002 (mmm-85) REVERT: P 56 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7145 (t) REVERT: Q 68 PHE cc_start: 0.6865 (m-80) cc_final: 0.6230 (m-80) REVERT: Z 85 GLU cc_start: 0.7542 (tt0) cc_final: 0.6936 (tp30) REVERT: Z 92 TYR cc_start: 0.7399 (t80) cc_final: 0.7079 (t80) REVERT: Z 96 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7811 (ptp-170) REVERT: Z 122 TRP cc_start: 0.8012 (m-10) cc_final: 0.7413 (m100) REVERT: Z 228 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4444 (tpt) REVERT: Z 282 PHE cc_start: 0.7901 (t80) cc_final: 0.7598 (t80) outliers start: 116 outliers final: 67 residues processed: 554 average time/residue: 0.5580 time to fit residues: 390.0360 Evaluate side-chains 532 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 452 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 205 ASN Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain S residue 152 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 112 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 29 SER Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 96 ARG Chi-restraints excluded: chain Z residue 205 ILE Chi-restraints excluded: chain Z residue 228 MET Chi-restraints excluded: chain Z residue 237 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 349 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 289 optimal weight: 0.4980 chunk 516 optimal weight: 6.9990 chunk 224 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 430 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 432 GLN D 218 GLN D 253 ASN D 442 ASN E 205 ASN E 253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.138900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085554 restraints weight = 68215.966| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.20 r_work: 0.3031 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 39961 Z= 0.142 Angle : 0.623 13.527 54301 Z= 0.317 Chirality : 0.044 0.297 6439 Planarity : 0.004 0.060 7149 Dihedral : 6.445 179.593 5891 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.39 % Allowed : 19.60 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.12), residues: 5299 helix: 1.72 (0.10), residues: 2855 sheet: -0.90 (0.21), residues: 623 loop : -0.68 (0.15), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 41 TYR 0.025 0.001 TYR W 113 PHE 0.049 0.001 PHE L 62 TRP 0.007 0.001 TRP Z 122 HIS 0.007 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00328 (39961) covalent geometry : angle 0.62294 (54301) hydrogen bonds : bond 0.04101 ( 2409) hydrogen bonds : angle 4.07795 ( 7053) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 476 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7936 (mmm-85) cc_final: 0.7668 (mmm-85) REVERT: A 177 ASP cc_start: 0.8851 (m-30) cc_final: 0.8633 (m-30) REVERT: A 497 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8238 (tpp80) REVERT: B 74 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8375 (mt-10) REVERT: B 85 ASP cc_start: 0.8272 (m-30) cc_final: 0.8010 (m-30) REVERT: B 179 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8036 (tp40) REVERT: B 225 MET cc_start: 0.9466 (tpt) cc_final: 0.9132 (tpt) REVERT: B 403 GLN cc_start: 0.7953 (mt0) cc_final: 0.7605 (mm-40) REVERT: B 422 LYS cc_start: 0.8608 (tttm) cc_final: 0.8193 (tppp) REVERT: C 13 LYS cc_start: 0.8975 (tttt) cc_final: 0.8767 (mtpt) REVERT: C 25 ARG cc_start: 0.7809 (tpp-160) cc_final: 0.7444 (tpp-160) REVERT: C 221 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8212 (ptt-90) REVERT: D 192 ASP cc_start: 0.7199 (m-30) cc_final: 0.6841 (m-30) REVERT: D 253 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7868 (t0) REVERT: D 467 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: E 1 MET cc_start: 0.6647 (mpp) cc_final: 0.5710 (ttm) REVERT: E 189 GLU cc_start: 0.8323 (tp30) cc_final: 0.8070 (tp30) REVERT: E 221 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8795 (mt-10) REVERT: E 337 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8160 (mm-30) REVERT: E 395 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: F 22 ASP cc_start: 0.8526 (p0) cc_final: 0.8178 (p0) REVERT: F 23 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8626 (mt-10) REVERT: F 92 ASN cc_start: 0.8477 (m-40) cc_final: 0.8151 (m110) REVERT: F 126 GLN cc_start: 0.9087 (tt0) cc_final: 0.8728 (tm-30) REVERT: F 204 GLU cc_start: 0.7718 (pp20) cc_final: 0.7167 (pp20) REVERT: F 312 ASP cc_start: 0.8806 (t0) cc_final: 0.8487 (t0) REVERT: F 355 ASP cc_start: 0.8619 (t70) cc_final: 0.8229 (t0) REVERT: F 431 LYS cc_start: 0.8788 (tttt) cc_final: 0.8457 (tptp) REVERT: F 467 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: G 50 ARG cc_start: 0.8314 (tmt170) cc_final: 0.7937 (tpt-90) REVERT: G 112 MET cc_start: 0.8754 (ttp) cc_final: 0.8511 (ttm) REVERT: G 245 MET cc_start: 0.9202 (ttt) cc_final: 0.8968 (ttt) REVERT: R 21 MET cc_start: 0.7170 (tpt) cc_final: 0.6923 (tpp) REVERT: R 48 GLU cc_start: 0.8813 (tt0) cc_final: 0.8215 (tt0) REVERT: R 60 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.5066 (t80) REVERT: S 102 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7720 (mttp) REVERT: S 104 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.6643 (tpm-80) REVERT: S 107 ARG cc_start: 0.9285 (mtt180) cc_final: 0.8553 (mtm-85) REVERT: Y 34 MET cc_start: 0.8680 (mmp) cc_final: 0.8209 (mtm) REVERT: V 57 GLN cc_start: 0.8003 (tp40) cc_final: 0.7778 (mm-40) REVERT: V 78 LYS cc_start: 0.8936 (tttp) cc_final: 0.8692 (ttpt) REVERT: V 128 ILE cc_start: 0.8700 (mm) cc_final: 0.8459 (mp) REVERT: V 138 ARG cc_start: 0.7716 (tpp-160) cc_final: 0.7367 (tpp-160) REVERT: W 136 ASP cc_start: 0.8396 (m-30) cc_final: 0.8082 (m-30) REVERT: W 137 GLN cc_start: 0.8668 (mm110) cc_final: 0.8247 (mm-40) REVERT: W 152 ARG cc_start: 0.5849 (mtp-110) cc_final: 0.3643 (mpt180) REVERT: H 66 ILE cc_start: 0.3357 (tt) cc_final: 0.3108 (tt) REVERT: I 1 MET cc_start: 0.3617 (tmt) cc_final: 0.3299 (tmt) REVERT: I 35 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.6923 (tp) REVERT: J 5 ASN cc_start: 0.6327 (p0) cc_final: 0.6040 (p0) REVERT: K 33 GLN cc_start: 0.7609 (mm-40) cc_final: 0.7350 (mm110) REVERT: K 37 ARG cc_start: 0.8403 (mpt-90) cc_final: 0.8073 (mpt90) REVERT: K 48 TYR cc_start: 0.6853 (m-80) cc_final: 0.6609 (m-80) REVERT: K 49 MET cc_start: 0.6968 (ttp) cc_final: 0.6641 (ttm) REVERT: K 70 ILE cc_start: 0.4294 (tt) cc_final: 0.3993 (mt) REVERT: L 44 ARG cc_start: 0.6591 (mtp85) cc_final: 0.5765 (mtt180) REVERT: L 48 TYR cc_start: 0.7264 (m-80) cc_final: 0.6371 (m-80) REVERT: M 57 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7518 (mm-30) REVERT: N 5 ASN cc_start: 0.7127 (p0) cc_final: 0.6923 (p0) REVERT: O 1 MET cc_start: 0.3247 (tpp) cc_final: 0.2788 (tpt) REVERT: O 50 PHE cc_start: 0.6270 (OUTLIER) cc_final: 0.6066 (t80) REVERT: P 1 MET cc_start: 0.5762 (tpp) cc_final: 0.4865 (mmt) REVERT: P 35 ILE cc_start: 0.8026 (tt) cc_final: 0.7589 (mt) REVERT: P 44 ARG cc_start: 0.5403 (tpt170) cc_final: 0.4982 (mmm-85) REVERT: P 56 THR cc_start: 0.7462 (OUTLIER) cc_final: 0.7144 (t) REVERT: Q 68 PHE cc_start: 0.6802 (m-80) cc_final: 0.6198 (m-80) REVERT: Z 85 GLU cc_start: 0.7530 (tt0) cc_final: 0.6855 (tp30) REVERT: Z 92 TYR cc_start: 0.7407 (t80) cc_final: 0.7184 (t80) REVERT: Z 122 TRP cc_start: 0.8026 (m-10) cc_final: 0.7420 (m100) REVERT: Z 228 MET cc_start: 0.5075 (tmt) cc_final: 0.4758 (tpt) REVERT: Z 239 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7147 (pt0) REVERT: Z 282 PHE cc_start: 0.7827 (t80) cc_final: 0.7565 (t80) outliers start: 91 outliers final: 52 residues processed: 533 average time/residue: 0.5865 time to fit residues: 392.8638 Evaluate side-chains 527 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 464 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 112 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 50 PHE Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain Q residue 49 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 427 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 491 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 333 optimal weight: 0.8980 chunk 226 optimal weight: 0.9990 chunk 517 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 432 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 442 ASN E 205 ASN E 253 ASN S 117 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.138189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.084929 restraints weight = 68151.248| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.16 r_work: 0.3010 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 39961 Z= 0.174 Angle : 0.641 13.693 54301 Z= 0.326 Chirality : 0.045 0.298 6439 Planarity : 0.004 0.059 7149 Dihedral : 6.443 179.456 5891 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.05 % Allowed : 20.28 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.12), residues: 5299 helix: 1.69 (0.10), residues: 2863 sheet: -0.89 (0.21), residues: 622 loop : -0.70 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 146 TYR 0.031 0.001 TYR J 48 PHE 0.019 0.001 PHE L 62 TRP 0.011 0.001 TRP Z 122 HIS 0.004 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00411 (39961) covalent geometry : angle 0.64065 (54301) hydrogen bonds : bond 0.04140 ( 2409) hydrogen bonds : angle 4.09516 ( 7053) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10598 Ramachandran restraints generated. 5299 Oldfield, 0 Emsley, 5299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 459 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7698 (mmm-85) REVERT: A 177 ASP cc_start: 0.8848 (m-30) cc_final: 0.8631 (m-30) REVERT: A 403 GLN cc_start: 0.8499 (mt0) cc_final: 0.8197 (tt0) REVERT: A 497 ARG cc_start: 0.8763 (mmm-85) cc_final: 0.8279 (tpp80) REVERT: B 74 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8389 (mt-10) REVERT: B 85 ASP cc_start: 0.8326 (m-30) cc_final: 0.8057 (m-30) REVERT: B 179 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: B 225 MET cc_start: 0.9511 (tpt) cc_final: 0.9136 (tpt) REVERT: B 403 GLN cc_start: 0.7969 (mt0) cc_final: 0.7620 (mm-40) REVERT: B 422 LYS cc_start: 0.8640 (tttm) cc_final: 0.8224 (tppp) REVERT: C 25 ARG cc_start: 0.7789 (tpp-160) cc_final: 0.7423 (tpp-160) REVERT: C 221 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8237 (ptt-90) REVERT: D 450 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: D 467 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: E 1 MET cc_start: 0.6747 (mpp) cc_final: 0.5838 (ttm) REVERT: E 189 GLU cc_start: 0.8373 (tp30) cc_final: 0.8171 (tp30) REVERT: E 221 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8783 (mt-10) REVERT: E 253 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8577 (t0) REVERT: E 337 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8251 (mm-30) REVERT: E 389 MET cc_start: 0.8417 (mtm) cc_final: 0.7754 (tpp) REVERT: E 395 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (pp20) REVERT: F 22 ASP cc_start: 0.8533 (p0) cc_final: 0.8184 (p0) REVERT: F 23 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8659 (mt-10) REVERT: F 92 ASN cc_start: 0.8454 (m-40) cc_final: 0.8146 (m110) REVERT: F 126 GLN cc_start: 0.9111 (tt0) cc_final: 0.8742 (tm-30) REVERT: F 204 GLU cc_start: 0.7786 (pp20) cc_final: 0.7218 (pp20) REVERT: F 312 ASP cc_start: 0.8804 (t0) cc_final: 0.8489 (t0) REVERT: F 355 ASP cc_start: 0.8617 (t70) cc_final: 0.8218 (t0) REVERT: F 431 LYS cc_start: 0.8776 (tttt) cc_final: 0.8459 (tptp) REVERT: G 50 ARG cc_start: 0.8298 (tmt170) cc_final: 0.7873 (tpt-90) REVERT: G 112 MET cc_start: 0.8750 (ttp) cc_final: 0.8535 (ttm) REVERT: G 245 MET cc_start: 0.9209 (ttt) cc_final: 0.8979 (ttt) REVERT: R 21 MET cc_start: 0.7161 (tpt) cc_final: 0.6932 (tpp) REVERT: R 48 GLU cc_start: 0.8820 (tt0) cc_final: 0.8217 (tt0) REVERT: R 60 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5023 (t80) REVERT: R 94 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8648 (pp30) REVERT: S 102 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7746 (mttp) REVERT: S 104 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.6614 (tpm-80) REVERT: S 107 ARG cc_start: 0.9298 (mtt180) cc_final: 0.8572 (mtm-85) REVERT: V 78 LYS cc_start: 0.8968 (tttp) cc_final: 0.8728 (ttpt) REVERT: V 112 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8288 (mp10) REVERT: V 138 ARG cc_start: 0.7742 (tpp-160) cc_final: 0.7377 (tpp-160) REVERT: W 103 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: W 136 ASP cc_start: 0.8417 (m-30) cc_final: 0.8105 (m-30) REVERT: W 137 GLN cc_start: 0.8643 (mm110) cc_final: 0.8224 (mm-40) REVERT: W 152 ARG cc_start: 0.5508 (mtp-110) cc_final: 0.3554 (mpt180) REVERT: H 66 ILE cc_start: 0.3239 (tt) cc_final: 0.3004 (tt) REVERT: I 35 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6876 (tp) REVERT: I 50 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: J 5 ASN cc_start: 0.6322 (p0) cc_final: 0.6036 (p0) REVERT: K 33 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7309 (mm110) REVERT: K 37 ARG cc_start: 0.8385 (mpt-90) cc_final: 0.8024 (mpt90) REVERT: K 70 ILE cc_start: 0.4339 (tt) cc_final: 0.4056 (mt) REVERT: L 44 ARG cc_start: 0.6520 (mtp85) cc_final: 0.5680 (mtp180) REVERT: L 48 TYR cc_start: 0.7239 (m-80) cc_final: 0.6068 (m-80) REVERT: O 1 MET cc_start: 0.3143 (tpp) cc_final: 0.2702 (tpt) REVERT: O 50 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.6045 (t80) REVERT: P 1 MET cc_start: 0.5638 (tpp) cc_final: 0.4787 (mmt) REVERT: P 35 ILE cc_start: 0.8059 (tt) cc_final: 0.7634 (mt) REVERT: P 44 ARG cc_start: 0.5271 (tpt170) cc_final: 0.4858 (mmm-85) REVERT: P 56 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7322 (t) REVERT: Q 68 PHE cc_start: 0.6807 (m-80) cc_final: 0.6211 (m-80) REVERT: Z 85 GLU cc_start: 0.7486 (tt0) cc_final: 0.6848 (tp30) REVERT: Z 122 TRP cc_start: 0.8061 (m-10) cc_final: 0.7463 (m100) REVERT: Z 228 MET cc_start: 0.5029 (OUTLIER) cc_final: 0.4143 (tpt) REVERT: Z 242 LYS cc_start: 0.9022 (ptpt) cc_final: 0.8784 (ptpp) REVERT: Z 255 PHE cc_start: 0.8959 (t80) cc_final: 0.8551 (t80) REVERT: Z 282 PHE cc_start: 0.7768 (t80) cc_final: 0.7549 (t80) outliers start: 78 outliers final: 52 residues processed: 510 average time/residue: 0.5821 time to fit residues: 373.3794 Evaluate side-chains 525 residues out of total 4270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 458 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 467 GLU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain E residue 341 PHE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 195 HIS Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 467 GLU Chi-restraints excluded: chain G residue 32 MET Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 60 PHE Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 23 PHE Chi-restraints excluded: chain V residue 112 GLN Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain W residue 103 GLU Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 32 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain O residue 50 PHE Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 56 THR Chi-restraints excluded: chain P residue 70 ILE Chi-restraints excluded: chain Q residue 49 MET Chi-restraints excluded: chain Z residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 6 optimal weight: 4.9990 chunk 289 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 506 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 312 optimal weight: 6.9990 chunk 366 optimal weight: 0.0270 chunk 97 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 HIS C 432 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN D 442 ASN E 205 ASN E 253 ASN S 117 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085487 restraints weight = 68097.508| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.18 r_work: 0.3022 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 39961 Z= 0.153 Angle : 0.700 42.338 54301 Z= 0.369 Chirality : 0.046 0.499 6439 Planarity : 0.005 0.109 7149 Dihedral : 6.424 179.703 5889 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.13 % Allowed : 20.42 % Favored : 77.45 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.12), residues: 5299 helix: 1.69 (0.10), residues: 2863 sheet: -0.90 (0.21), residues: 622 loop : -0.66 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 41 TYR 0.040 0.001 TYR K 48 PHE 0.028 0.001 PHE L 62 TRP 0.009 0.001 TRP Z 122 HIS 0.004 0.001 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00361 (39961) covalent geometry : angle 0.70006 (54301) hydrogen bonds : bond 0.04124 ( 2409) hydrogen bonds : angle 4.11441 ( 7053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18036.81 seconds wall clock time: 306 minutes 25.73 seconds (18385.73 seconds total)