Starting phenix.real_space_refine on Sat Mar 7 06:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.map" model { file = "/net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r0w_4699/03_2026/6r0w_4699.cif" } resolution = 3.6 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= 0.004 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 103 5.16 5 C 25044 2.51 5 N 7293 2.21 5 O 7736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40181 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 433} Chain: "E" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3616 Classifications: {'peptide': 462} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 435} Chain: "F" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3626 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 436} Chain: "G" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1628 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 808 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1437 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 7, 'TRANS': 178} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1575 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1248 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'ASP:plan': 20, 'PHE:plan': 15, 'TYR:plan': 7, 'ASN:plan1': 4, 'ARG:plan': 35, 'GLU:plan': 26, 'GLN:plan1': 12, 'HIS:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 566 Chain: "N" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 3190 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PTRANS': 36, 'TRANS': 612} Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 2030 Unresolved non-hydrogen angles: 2628 Unresolved non-hydrogen dihedrals: 1714 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLU:plan': 56, 'ARG:plan': 37, 'GLN:plan1': 17, 'HIS:plan': 21, 'TYR:plan': 18, 'TRP:plan': 12, 'PHE:plan': 33, 'ASP:plan': 12, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 1071 Chain: "O" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Q" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 356 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "S" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "U" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "V" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "W" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "X" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 347 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Y" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "Z" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 351 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.93, per 1000 atoms: 0.25 Number of scatterers: 40181 At special positions: 0 Unit cell: (149.73, 148.645, 257.145, 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 103 16.00 P 4 15.00 Mg 1 11.99 O 7736 8.00 N 7293 7.00 C 25044 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: 3.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10540 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 36 sheets defined 56.8% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 295 through 315 removed outlier: 5.115A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.674A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.722A pdb=" N ALA A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 464 removed outlier: 3.636A pdb=" N LEU A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 508 through 530 removed outlier: 3.706A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.746A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.890A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.960A pdb=" N MET B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 297 through 316 removed outlier: 4.196A pdb=" N ALA B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.641A pdb=" N ARG B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 removed outlier: 3.718A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 443 Processing helix chain 'B' and resid 446 through 471 removed outlier: 4.307A pdb=" N GLU B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 removed outlier: 4.060A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.589A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.804A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 259 through 269 removed outlier: 4.980A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.429A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.728A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.595A pdb=" N TYR C 350 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 352 No H-bonds generated for 'chain 'C' and resid 351 through 352' Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 471 removed outlier: 4.578A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 542 removed outlier: 3.959A pdb=" N LEU C 540 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN C 541 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 Processing helix chain 'C' and resid 551 through 554 removed outlier: 3.663A pdb=" N VAL C 554 " --> pdb=" O ALA C 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 558 through 573 removed outlier: 3.635A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.762A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.923A pdb=" N LEU D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.522A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 249 removed outlier: 3.821A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.889A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.862A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 345 removed outlier: 3.645A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 399 removed outlier: 3.970A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.961A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 445 through 446 No H-bonds generated for 'chain 'D' and resid 445 through 446' Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 455 through 462 removed outlier: 3.677A pdb=" N ILE D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 200 through 212 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 233 through 248 Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.827A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.515A pdb=" N ARG E 345 " --> pdb=" O ARG E 341 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS E 346 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.962A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.768A pdb=" N LEU E 395 " --> pdb=" O ASP E 391 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.688A pdb=" N ASP E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 461 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.809A pdb=" N ARG F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.695A pdb=" N LEU F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU F 209 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 212 " --> pdb=" O PHE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 249 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 4.069A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 347 Processing helix chain 'F' and resid 374 through 400 removed outlier: 4.025A pdb=" N ASP F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE F 392 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.874A pdb=" N LEU F 404 " --> pdb=" O GLU F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 406 through 422 removed outlier: 4.125A pdb=" N ARG F 420 " --> pdb=" O ASP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 removed outlier: 3.565A pdb=" N ILE F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.981A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 removed outlier: 3.607A pdb=" N GLY G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 169 removed outlier: 3.517A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 206 removed outlier: 4.119A pdb=" N LYS G 195 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG G 204 " --> pdb=" O LYS G 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 17 removed outlier: 4.160A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 19 through 106 removed outlier: 4.271A pdb=" N GLU I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 removed outlier: 3.863A pdb=" N ALA I 110 " --> pdb=" O ARG I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 93 removed outlier: 4.686A pdb=" N GLU J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 4.252A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 132 removed outlier: 3.628A pdb=" N GLU J 132 " --> pdb=" O LEU J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 187 removed outlier: 5.970A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 104 removed outlier: 4.629A pdb=" N GLN K 32 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 removed outlier: 3.921A pdb=" N VAL K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 91 removed outlier: 6.037A pdb=" N GLN L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L 80 " --> pdb=" O ARG L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 114 Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.655A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 5.140A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN L 184 " --> pdb=" O SER L 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 18 removed outlier: 3.749A pdb=" N ARG M 11 " --> pdb=" O TYR M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 27 removed outlier: 3.849A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 33 through 43 Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.856A pdb=" N GLU M 48 " --> pdb=" O TYR M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 70 Processing helix chain 'M' and resid 78 through 86 removed outlier: 4.163A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 106 Processing helix chain 'M' and resid 120 through 127 removed outlier: 3.569A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.632A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 182 Processing helix chain 'M' and resid 187 through 207 Processing helix chain 'M' and resid 213 through 218 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 238 through 243 Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 279 Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'M' and resid 316 through 320 removed outlier: 3.962A pdb=" N VAL M 320 " --> pdb=" O GLU M 317 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 27 Processing helix chain 'N' and resid 46 through 71 Processing helix chain 'N' and resid 83 through 118 Proline residue: N 93 - end of helix removed outlier: 3.626A pdb=" N TYR N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 128 Processing helix chain 'N' and resid 149 through 160 removed outlier: 3.825A pdb=" N VAL N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 198 Processing helix chain 'N' and resid 212 through 267 Proline residue: N 228 - end of helix removed outlier: 6.086A pdb=" N SER N 247 " --> pdb=" O ARG N 243 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR N 248 " --> pdb=" O GLU N 244 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 285 No H-bonds generated for 'chain 'N' and resid 283 through 285' Processing helix chain 'N' and resid 286 through 295 Processing helix chain 'N' and resid 330 through 335 removed outlier: 3.694A pdb=" N VAL N 334 " --> pdb=" O PHE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 363 Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 365 through 385 Processing helix chain 'N' and resid 399 through 425 removed outlier: 3.505A pdb=" N ILE N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP N 416 " --> pdb=" O TRP N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 489 Processing helix chain 'N' and resid 491 through 516 removed outlier: 3.730A pdb=" N PHE N 495 " --> pdb=" O HIS N 491 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 543 removed outlier: 4.760A pdb=" N GLY N 526 " --> pdb=" O GLY N 522 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU N 527 " --> pdb=" O TRP N 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 560 Processing helix chain 'N' and resid 561 through 588 removed outlier: 4.367A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) Processing helix chain 'N' and resid 593 through 632 removed outlier: 5.287A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix removed outlier: 4.019A pdb=" N PHE N 629 " --> pdb=" O TRP N 625 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR N 630 " --> pdb=" O VAL N 626 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 48 removed outlier: 3.504A pdb=" N GLY O 13 " --> pdb=" O GLY O 9 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 63 through 80 Processing helix chain 'P' and resid 10 through 48 removed outlier: 3.573A pdb=" N LEU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 62 through 79 removed outlier: 4.188A pdb=" N VAL P 66 " --> pdb=" O PRO P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 48 removed outlier: 4.133A pdb=" N ARG Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 Processing helix chain 'Q' and resid 62 through 79 removed outlier: 4.277A pdb=" N VAL Q 66 " --> pdb=" O PRO Q 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 48 removed outlier: 4.078A pdb=" N ARG R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 removed outlier: 4.490A pdb=" N ILE R 57 " --> pdb=" O GLY R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.179A pdb=" N VAL R 66 " --> pdb=" O PRO R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 48 removed outlier: 4.153A pdb=" N ARG S 36 " --> pdb=" O VAL S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 61 Processing helix chain 'S' and resid 62 through 80 removed outlier: 4.316A pdb=" N VAL S 66 " --> pdb=" O PRO S 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 48 removed outlier: 3.701A pdb=" N ILE T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU T 25 " --> pdb=" O LEU T 21 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG T 36 " --> pdb=" O VAL T 32 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE T 37 " --> pdb=" O ALA T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 removed outlier: 3.510A pdb=" N ALA T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 80 removed outlier: 4.367A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 48 removed outlier: 4.141A pdb=" N ARG U 36 " --> pdb=" O VAL U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 80 removed outlier: 4.543A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 48 removed outlier: 4.428A pdb=" N GLY V 13 " --> pdb=" O GLY V 9 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG V 36 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE V 37 " --> pdb=" O ALA V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 61 Processing helix chain 'V' and resid 63 through 80 Processing helix chain 'W' and resid 11 through 48 removed outlier: 4.176A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 61 Processing helix chain 'W' and resid 62 through 80 removed outlier: 4.437A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 48 removed outlier: 4.221A pdb=" N LEU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE X 15 " --> pdb=" O ASP X 11 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA X 16 " --> pdb=" O ARG X 12 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 Processing helix chain 'X' and resid 63 through 80 Processing helix chain 'Y' and resid 11 through 48 removed outlier: 4.263A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 63 through 79 Processing helix chain 'Z' and resid 9 through 48 removed outlier: 3.908A pdb=" N GLY Z 13 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 63 through 80 Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 14 removed outlier: 4.998A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 removed outlier: 6.287A pdb=" N GLY A 82 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA A 289 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR A 84 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR A 291 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 197 " --> pdb=" O ILE A 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 4.136A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 removed outlier: 4.750A pdb=" N GLU A 159 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 10 removed outlier: 5.332A pdb=" N ILE B 6 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS B 17 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.767A pdb=" N TYR E 13 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL E 50 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 75 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LYS E 6 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN J 165 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.303A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B 367 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 197 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.303A pdb=" N GLY B 82 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA B 289 " --> pdb=" O GLY B 82 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR B 84 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 251 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP B 325 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL B 253 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA B 224 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL B 384 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 226 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB5, first strand: chain 'B' and resid 120 through 121 removed outlier: 4.268A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 10 removed outlier: 6.570A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB9, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.472A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C 255 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 381 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 322 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA C 383 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 324 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 82 through 84 removed outlier: 6.472A pdb=" N GLY C 82 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ALA C 289 " --> pdb=" O GLY C 82 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR C 84 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C 255 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL C 381 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 322 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA C 383 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ALA C 324 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 143 through 148 removed outlier: 6.735A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.683A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 18 through 22 removed outlier: 6.843A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AC6, first strand: chain 'D' and resid 92 through 93 removed outlier: 3.678A pdb=" N LEU D 221 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE D 311 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL D 255 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE D 313 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 257 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N SER D 315 " --> pdb=" O LEU D 257 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE D 152 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC8, first strand: chain 'E' and resid 92 through 94 removed outlier: 6.115A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 15 removed outlier: 4.957A pdb=" N TYR F 13 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 32 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AD2, first strand: chain 'F' and resid 92 through 93 removed outlier: 5.623A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL F 218 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR F 258 " --> pdb=" O VAL F 190 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA F 192 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AD4, first strand: chain 'H' and resid 20 through 21 removed outlier: 6.175A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 141 through 144 removed outlier: 4.016A pdb=" N VAL L 152 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 31 through 32 Processing sheet with id=AD7, first strand: chain 'N' and resid 31 through 32 Processing sheet with id=AD8, first strand: chain 'N' and resid 141 through 145 Processing sheet with id=AD9, first strand: chain 'N' and resid 389 through 391 2718 hydrogen bonds defined for protein. 7932 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: 10.29 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8120 1.32 - 1.44: 8905 1.44 - 1.56: 23496 1.56 - 1.69: 7 1.69 - 1.81: 194 Bond restraints: 40722 Sorted by residual: bond pdb=" CA GLU F 7 " pdb=" C GLU F 7 " ideal model delta sigma weight residual 1.524 1.478 0.047 1.22e-02 6.72e+03 1.46e+01 bond pdb=" CB TYR I 73 " pdb=" CG TYR I 73 " ideal model delta sigma weight residual 1.512 1.434 0.078 2.20e-02 2.07e+03 1.26e+01 bond pdb=" CB TYR F 8 " pdb=" CG TYR F 8 " ideal model delta sigma weight residual 1.512 1.438 0.074 2.20e-02 2.07e+03 1.13e+01 bond pdb=" CG LEU B 322 " pdb=" CD1 LEU B 322 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.12e+01 bond pdb=" CB GLN J 162 " pdb=" CG GLN J 162 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.11e+01 ... (remaining 40717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 53713 3.26 - 6.51: 1451 6.51 - 9.77: 163 9.77 - 13.02: 29 13.02 - 16.28: 7 Bond angle restraints: 55363 Sorted by residual: angle pdb=" N GLY N 275 " pdb=" CA GLY N 275 " pdb=" C GLY N 275 " ideal model delta sigma weight residual 111.37 102.30 9.07 1.29e+00 6.01e-01 4.94e+01 angle pdb=" N GLY C 366 " pdb=" CA GLY C 366 " pdb=" C GLY C 366 " ideal model delta sigma weight residual 113.18 129.46 -16.28 2.37e+00 1.78e-01 4.72e+01 angle pdb=" N GLY F 179 " pdb=" CA GLY F 179 " pdb=" C GLY F 179 " ideal model delta sigma weight residual 111.36 104.75 6.61 1.17e+00 7.31e-01 3.19e+01 angle pdb=" N ILE K 23 " pdb=" CA ILE K 23 " pdb=" C ILE K 23 " ideal model delta sigma weight residual 111.81 107.14 4.67 8.60e-01 1.35e+00 2.95e+01 angle pdb=" C ASN C 442 " pdb=" N VAL C 443 " pdb=" CA VAL C 443 " ideal model delta sigma weight residual 122.97 117.71 5.26 9.80e-01 1.04e+00 2.88e+01 ... (remaining 55358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.48: 24271 32.48 - 64.95: 207 64.95 - 97.43: 8 97.43 - 129.91: 0 129.91 - 162.38: 1 Dihedral angle restraints: 24487 sinusoidal: 7995 harmonic: 16492 Sorted by residual: dihedral pdb=" CA ALA H 43 " pdb=" C ALA H 43 " pdb=" N LEU H 44 " pdb=" CA LEU H 44 " ideal model delta harmonic sigma weight residual 180.00 138.92 41.08 0 5.00e+00 4.00e-02 6.75e+01 dihedral pdb=" CA VAL N 301 " pdb=" C VAL N 301 " pdb=" N VAL N 302 " pdb=" CA VAL N 302 " ideal model delta harmonic sigma weight residual 180.00 -142.00 -38.00 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" CA PHE G 108 " pdb=" C PHE G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta harmonic sigma weight residual 180.00 143.49 36.51 0 5.00e+00 4.00e-02 5.33e+01 ... (remaining 24484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5254 0.087 - 0.174: 1049 0.174 - 0.262: 99 0.262 - 0.349: 15 0.349 - 0.436: 3 Chirality restraints: 6420 Sorted by residual: chirality pdb=" CB ILE F 229 " pdb=" CA ILE F 229 " pdb=" CG1 ILE F 229 " pdb=" CG2 ILE F 229 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CB ILE C 226 " pdb=" CA ILE C 226 " pdb=" CG1 ILE C 226 " pdb=" CG2 ILE C 226 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASP E 259 " pdb=" N ASP E 259 " pdb=" C ASP E 259 " pdb=" CB ASP E 259 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 6417 not shown) Planarity restraints: 7461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO B 227 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA L 40 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA L 40 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA L 40 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU L 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 393 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO B 394 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 394 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 394 " 0.044 5.00e-02 4.00e+02 ... (remaining 7458 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1369 2.68 - 3.23: 38608 3.23 - 3.79: 65040 3.79 - 4.34: 77043 4.34 - 4.90: 132749 Nonbonded interactions: 314809 Sorted by model distance: nonbonded pdb=" O GLU L 36 " pdb=" O LYS L 39 " model vdw 2.125 2.432 nonbonded pdb=" OE1 GLU C 38 " pdb=" OH TYR C 52 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 263 " pdb=" O ARG F 124 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU B 38 " pdb=" OH TYR B 52 " model vdw 2.268 3.040 nonbonded pdb=" O ASP D 67 " pdb=" OG1 THR D 71 " model vdw 2.277 3.040 ... (remaining 314804 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' selection = chain 'B' selection = (chain 'C' and resid 1 through 577) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 5 through 464) selection = (chain 'F' and resid 5 through 464) } ncs_group { reference = (chain 'I' and resid 22 through 120) selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'O' and resid 9 through 80) selection = (chain 'P' and resid 9 through 80) selection = (chain 'Q' and resid 9 through 80) selection = (chain 'R' and resid 9 through 80) selection = (chain 'S' and resid 9 through 80) selection = (chain 'T' and resid 9 through 80) selection = (chain 'U' and resid 9 through 80) selection = (chain 'V' and resid 9 through 80) selection = (chain 'W' and resid 9 through 80) selection = chain 'X' selection = (chain 'Y' and resid 9 through 80) selection = (chain 'Z' and resid 9 through 80) } 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 group one per residue 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: 0.180 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: 0.060 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 40.850 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.120 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.015 0.141 40722 Z= 0.630 Angle : 1.256 16.277 55363 Z= 0.671 Chirality : 0.068 0.436 6420 Planarity : 0.008 0.099 7461 Dihedral : 10.437 162.385 13947 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.16 % Favored : 91.78 % Rotamer: Outliers : 0.65 % Allowed : 5.58 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -3.98 (0.09), residues: 5794 helix: -2.25 (0.06), residues: 3174 sheet: -2.21 (0.20), residues: 596 loop : -3.15 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 146 TYR 0.044 0.004 TYR D 251 PHE 0.043 0.005 PHE C 205 TRP 0.040 0.005 TRP C 407 HIS 0.022 0.004 HIS F 458 Details of bonding type rmsd covalent geometry : bond 0.01489 (40722) covalent geometry : angle 1.25563 (55363) hydrogen bonds : bond 0.11168 ( 2696) hydrogen bonds : angle 6.30487 ( 7932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 889 time to evaluate : 1.477 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: A 50 GLN cc_start: 0.9229 (tp40) cc_final: 0.9027 (tt0) REVERT: A 92 GLU cc_start: 0.8884 (tp30) cc_final: 0.8556 (mt-10) REVERT: A 504 ASP cc_start: 0.8582 (t70) cc_final: 0.8354 (t70) REVERT: A 547 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7357 (mtp180) REVERT: A 568 LYS cc_start: 0.9203 (mptm) cc_final: 0.8555 (pttp) REVERT: B 25 TYR cc_start: 0.8986 (m-80) cc_final: 0.8727 (m-80) REVERT: B 81 ASN cc_start: 0.8840 (t0) cc_final: 0.8539 (t0) REVERT: B 127 ASP cc_start: 0.8766 (m-30) cc_final: 0.8332 (m-30) REVERT: B 133 MET cc_start: 0.9194 (ttm) cc_final: 0.8911 (tpp) REVERT: B 156 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8478 (ttt-90) REVERT: B 176 GLU cc_start: 0.8680 (tt0) cc_final: 0.8479 (tp30) REVERT: B 213 ASP cc_start: 0.9418 (p0) cc_final: 0.9148 (p0) REVERT: B 261 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8949 (mt-10) REVERT: B 325 ASP cc_start: 0.8601 (t70) cc_final: 0.8291 (t70) REVERT: B 375 GLU cc_start: 0.9214 (pp20) cc_final: 0.8998 (pp20) REVERT: B 493 ASP cc_start: 0.8929 (t0) cc_final: 0.8308 (m-30) REVERT: B 524 LYS cc_start: 0.9237 (tmmt) cc_final: 0.8929 (tppt) REVERT: B 557 GLU cc_start: 0.9257 (tt0) cc_final: 0.8849 (tp30) REVERT: B 558 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8716 (tp30) REVERT: C 1 MET cc_start: 0.7922 (tmm) cc_final: 0.7621 (tmm) REVERT: C 27 ILE cc_start: 0.9513 (mm) cc_final: 0.9287 (mm) REVERT: C 41 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8776 (tmm-80) REVERT: C 441 GLU cc_start: 0.9475 (tp30) cc_final: 0.8991 (mm-30) REVERT: C 442 ASN cc_start: 0.9263 (m110) cc_final: 0.8651 (t0) REVERT: C 524 LYS cc_start: 0.9286 (ttpp) cc_final: 0.8918 (tmtt) REVERT: D 6 LYS cc_start: 0.8955 (tptm) cc_final: 0.8737 (tppt) REVERT: D 8 TYR cc_start: 0.8893 (m-80) cc_final: 0.8059 (m-80) REVERT: D 49 GLU cc_start: 0.9068 (tt0) cc_final: 0.8715 (tm-30) REVERT: D 222 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8094 (t0) REVERT: D 223 LYS cc_start: 0.8669 (pttm) cc_final: 0.8132 (tptp) REVERT: D 226 ASP cc_start: 0.8711 (p0) cc_final: 0.8400 (p0) REVERT: D 376 LYS cc_start: 0.8753 (ttpm) cc_final: 0.8344 (tptm) REVERT: E 62 GLU cc_start: 0.8961 (pt0) cc_final: 0.8607 (pm20) REVERT: E 275 GLU cc_start: 0.9234 (mp0) cc_final: 0.8892 (mt-10) REVERT: E 318 ASP cc_start: 0.8734 (t0) cc_final: 0.8461 (t0) REVERT: E 376 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8584 (ttpt) REVERT: E 411 TYR cc_start: 0.8495 (m-10) cc_final: 0.8051 (m-10) REVERT: E 450 GLU cc_start: 0.8691 (tp30) cc_final: 0.8366 (tm-30) REVERT: F 79 VAL cc_start: 0.9194 (p) cc_final: 0.8925 (m) REVERT: F 141 MET cc_start: 0.9094 (mtp) cc_final: 0.8837 (mtm) REVERT: F 176 ASP cc_start: 0.9284 (m-30) cc_final: 0.9082 (m-30) REVERT: F 315 SER cc_start: 0.8985 (m) cc_final: 0.8635 (p) REVERT: F 380 ASP cc_start: 0.9238 (m-30) cc_final: 0.9019 (t0) REVERT: G 61 TYR cc_start: 0.8831 (m-80) cc_final: 0.8533 (m-80) REVERT: G 68 GLN cc_start: 0.8150 (mt0) cc_final: 0.7754 (tm-30) REVERT: G 152 GLU cc_start: 0.8818 (pt0) cc_final: 0.8594 (tm-30) REVERT: G 208 GLU cc_start: 0.7529 (tp30) cc_final: 0.6801 (tt0) REVERT: H 52 LEU cc_start: 0.7102 (mp) cc_final: 0.6885 (mt) REVERT: H 61 ARG cc_start: 0.7951 (tmt-80) cc_final: 0.7334 (ttp80) REVERT: H 77 LEU cc_start: 0.6710 (pt) cc_final: 0.6438 (pt) REVERT: I 88 TYR cc_start: 0.7779 (m-10) cc_final: 0.7548 (m-80) REVERT: J 58 ARG cc_start: 0.8328 (mtm180) cc_final: 0.7226 (ttp-170) REVERT: J 97 LYS cc_start: 0.8948 (mttt) cc_final: 0.8675 (mtmt) REVERT: J 106 LYS cc_start: 0.8308 (mttt) cc_final: 0.8062 (tptt) REVERT: J 112 LEU cc_start: 0.8642 (mp) cc_final: 0.8066 (tt) REVERT: K 45 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7063 (tm-30) REVERT: L 11 GLU cc_start: 0.3136 (mt-10) cc_final: 0.2777 (mm-30) REVERT: L 61 GLU cc_start: 0.8543 (pt0) cc_final: 0.8008 (pt0) outliers start: 21 outliers final: 13 residues processed: 908 average time/residue: 0.3235 time to fit residues: 438.4025 Evaluate side-chains 627 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 613 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 145 HIS A 185 HIS A 239 GLN A 423 ASN A 571 GLN B 316 GLN C 316 GLN C 397 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 HIS D 425 GLN E 429 ASN F 428 GLN G 10 ASN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 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 = 0.3741 r_free = 0.3741 target = 0.134547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099359 restraints weight = 75504.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102558 restraints weight = 37249.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103329 restraints weight = 22903.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104611 restraints weight = 16581.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105721 restraints weight = 12148.103| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 40722 Z= 0.205 Angle : 0.720 15.253 55363 Z= 0.371 Chirality : 0.045 0.200 6420 Planarity : 0.006 0.080 7461 Dihedral : 6.351 142.301 6292 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 2.74 % Allowed : 12.33 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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 are not related in a simple way. whole: -1.69 (0.10), residues: 5794 helix: -0.01 (0.09), residues: 3207 sheet: -1.97 (0.20), residues: 595 loop : -2.64 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 74 TYR 0.020 0.002 TYR D 286 PHE 0.019 0.002 PHE C 269 TRP 0.020 0.002 TRP C 438 HIS 0.010 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00457 (40722) covalent geometry : angle 0.71951 (55363) hydrogen bonds : bond 0.04630 ( 2696) hydrogen bonds : angle 4.97114 ( 7932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 716 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASP cc_start: 0.8446 (p0) cc_final: 0.8205 (m-30) REVERT: A 504 ASP cc_start: 0.7728 (t70) cc_final: 0.7461 (t70) REVERT: A 568 LYS cc_start: 0.8735 (mptm) cc_final: 0.8382 (pttp) REVERT: B 25 TYR cc_start: 0.7872 (m-80) cc_final: 0.7319 (m-80) REVERT: B 40 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8201 (mt) REVERT: B 81 ASN cc_start: 0.8295 (t0) cc_final: 0.7874 (t0) REVERT: B 153 VAL cc_start: 0.8985 (t) cc_final: 0.8776 (t) REVERT: B 456 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 476 LEU cc_start: 0.8958 (mm) cc_final: 0.8692 (mp) REVERT: C 27 ILE cc_start: 0.9119 (mm) cc_final: 0.8849 (mm) REVERT: C 41 ARG cc_start: 0.8148 (tmm-80) cc_final: 0.7524 (ttt180) REVERT: C 341 LEU cc_start: 0.8953 (mt) cc_final: 0.8663 (mt) REVERT: C 442 ASN cc_start: 0.8637 (m110) cc_final: 0.8349 (t0) REVERT: D 49 GLU cc_start: 0.7865 (tt0) cc_final: 0.7330 (tm-30) REVERT: D 223 LYS cc_start: 0.8209 (pttm) cc_final: 0.7778 (tptp) REVERT: D 342 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8069 (tm-30) REVERT: D 362 MET cc_start: 0.8923 (ttp) cc_final: 0.8722 (ttp) REVERT: E 318 ASP cc_start: 0.8069 (t0) cc_final: 0.7777 (t0) REVERT: E 376 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7954 (mtpp) REVERT: E 411 TYR cc_start: 0.8145 (m-10) cc_final: 0.7860 (m-10) REVERT: F 94 ASN cc_start: 0.8130 (p0) cc_final: 0.7857 (p0) REVERT: F 295 TYR cc_start: 0.8768 (m-10) cc_final: 0.8518 (m-10) REVERT: F 315 SER cc_start: 0.8861 (m) cc_final: 0.8290 (p) REVERT: F 329 THR cc_start: 0.9429 (m) cc_final: 0.9114 (m) REVERT: G 50 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7907 (mtt-85) REVERT: G 68 GLN cc_start: 0.7707 (mt0) cc_final: 0.7427 (tm-30) REVERT: G 177 ARG cc_start: 0.8021 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: H 4 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8253 (pp) REVERT: H 19 GLU cc_start: 0.8094 (tp30) cc_final: 0.7430 (tm-30) REVERT: H 21 TYR cc_start: 0.8368 (m-10) cc_final: 0.7683 (m-10) REVERT: H 54 ASP cc_start: 0.7615 (p0) cc_final: 0.7043 (p0) REVERT: H 61 ARG cc_start: 0.7873 (tmt-80) cc_final: 0.7391 (ptm-80) REVERT: J 58 ARG cc_start: 0.8337 (mtm180) cc_final: 0.7114 (tmm-80) REVERT: J 100 TRP cc_start: 0.6350 (p-90) cc_final: 0.6038 (t60) REVERT: J 107 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7503 (pp) REVERT: J 112 LEU cc_start: 0.8102 (mp) cc_final: 0.7765 (tt) REVERT: J 153 ARG cc_start: 0.7020 (ptm-80) cc_final: 0.6580 (ptm-80) REVERT: K 45 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7205 (tm-30) REVERT: L 11 GLU cc_start: 0.2883 (mt-10) cc_final: 0.2619 (mm-30) REVERT: L 61 GLU cc_start: 0.8349 (pt0) cc_final: 0.8078 (pt0) REVERT: L 82 GLU cc_start: 0.8255 (tp30) cc_final: 0.7732 (tp30) REVERT: L 85 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7701 (ttp80) outliers start: 89 outliers final: 48 residues processed: 776 average time/residue: 0.2914 time to fit residues: 348.0005 Evaluate side-chains 660 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 608 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 429 ASN Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 533 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 516 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 446 optimal weight: 8.9990 chunk 454 optimal weight: 50.0000 chunk 51 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS D 338 GLN E 363 ASN E 427 GLN G 10 ASN G 185 GLN H 11 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098589 restraints weight = 75548.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101592 restraints weight = 37635.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.102570 restraints weight = 22071.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103671 restraints weight = 16670.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104354 restraints weight = 12566.035| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40722 Z= 0.217 Angle : 0.687 15.147 55363 Z= 0.352 Chirality : 0.045 0.187 6420 Planarity : 0.005 0.063 7461 Dihedral : 5.874 125.039 6290 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.30 % Favored : 93.68 % Rotamer: Outliers : 3.98 % Allowed : 14.18 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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 are not related in a simple way. whole: -0.72 (0.11), residues: 5794 helix: 0.94 (0.09), residues: 3217 sheet: -1.86 (0.20), residues: 632 loop : -2.42 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 74 TYR 0.017 0.002 TYR C 52 PHE 0.017 0.001 PHE C 205 TRP 0.014 0.001 TRP A 330 HIS 0.007 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00495 (40722) covalent geometry : angle 0.68725 (55363) hydrogen bonds : bond 0.04265 ( 2696) hydrogen bonds : angle 4.70495 ( 7932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 651 time to evaluate : 1.511 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 85 ASP cc_start: 0.8481 (p0) cc_final: 0.8213 (p0) REVERT: A 213 ASP cc_start: 0.8395 (p0) cc_final: 0.8191 (m-30) REVERT: A 238 GLN cc_start: 0.8654 (mt0) cc_final: 0.8240 (mt0) REVERT: A 423 ASN cc_start: 0.8774 (t0) cc_final: 0.8434 (t0) REVERT: A 504 ASP cc_start: 0.7902 (t70) cc_final: 0.7554 (t70) REVERT: A 568 LYS cc_start: 0.8720 (mptm) cc_final: 0.8336 (pttp) REVERT: B 8 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8654 (tttm) REVERT: B 40 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 81 ASN cc_start: 0.8328 (t0) cc_final: 0.7894 (t0) REVERT: B 153 VAL cc_start: 0.8976 (t) cc_final: 0.8756 (t) REVERT: B 337 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8931 (mm) REVERT: B 456 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 460 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7671 (ttm-80) REVERT: B 492 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7867 (mt-10) REVERT: B 506 TYR cc_start: 0.7924 (t80) cc_final: 0.7573 (t80) REVERT: C 27 ILE cc_start: 0.9163 (mm) cc_final: 0.8918 (mm) REVERT: C 41 ARG cc_start: 0.8205 (tmm-80) cc_final: 0.7525 (ttt180) REVERT: C 241 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8896 (mp) REVERT: C 442 ASN cc_start: 0.8736 (m110) cc_final: 0.8372 (t0) REVERT: C 520 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8956 (mm) REVERT: D 49 GLU cc_start: 0.7821 (tt0) cc_final: 0.7332 (tm-30) REVERT: D 167 ILE cc_start: 0.9206 (pt) cc_final: 0.8956 (mt) REVERT: D 223 LYS cc_start: 0.8136 (pttm) cc_final: 0.7802 (tptp) REVERT: D 342 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 318 ASP cc_start: 0.8037 (t0) cc_final: 0.7698 (t0) REVERT: F 94 ASN cc_start: 0.8148 (p0) cc_final: 0.7877 (p0) REVERT: F 315 SER cc_start: 0.8837 (m) cc_final: 0.8282 (p) REVERT: F 329 THR cc_start: 0.9416 (m) cc_final: 0.9161 (m) REVERT: G 50 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7828 (mtt-85) REVERT: G 61 TYR cc_start: 0.7997 (m-80) cc_final: 0.7660 (m-80) REVERT: G 68 GLN cc_start: 0.7442 (mt0) cc_final: 0.7084 (tm-30) REVERT: G 177 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: H 4 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8343 (pp) REVERT: H 9 THR cc_start: 0.7007 (m) cc_final: 0.6783 (p) REVERT: H 19 GLU cc_start: 0.8147 (tp30) cc_final: 0.7514 (tm-30) REVERT: H 21 TYR cc_start: 0.8324 (m-10) cc_final: 0.7663 (m-10) REVERT: H 54 ASP cc_start: 0.7563 (p0) cc_final: 0.7003 (p0) REVERT: H 61 ARG cc_start: 0.7793 (tmt-80) cc_final: 0.7276 (ttp-110) REVERT: J 58 ARG cc_start: 0.8246 (mtm180) cc_final: 0.7043 (tmm-80) REVERT: J 97 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7908 (mtmt) REVERT: J 100 TRP cc_start: 0.6446 (p-90) cc_final: 0.6071 (t60) REVERT: J 112 LEU cc_start: 0.8132 (mp) cc_final: 0.7839 (tp) REVERT: J 172 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: K 22 LEU cc_start: 0.0078 (OUTLIER) cc_final: -0.0246 (mm) REVERT: K 45 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7289 (tm-30) REVERT: L 82 GLU cc_start: 0.8288 (tp30) cc_final: 0.7803 (tp30) REVERT: L 85 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7721 (ttp80) outliers start: 129 outliers final: 75 residues processed: 745 average time/residue: 0.2868 time to fit residues: 331.3572 Evaluate side-chains 662 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 579 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 172 ASP Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 202 optimal weight: 8.9990 chunk 361 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 563 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 426 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 423 optimal weight: 40.0000 chunk 386 optimal weight: 10.0000 overall best weight: 7.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 496 GLN C 571 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS E 427 GLN E 429 ASN F 262 ASN F 428 GLN ** G 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097646 restraints weight = 75542.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.100862 restraints weight = 37700.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101679 restraints weight = 21545.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102701 restraints weight = 16467.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.103987 restraints weight = 12406.906| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 40722 Z= 0.253 Angle : 0.699 18.384 55363 Z= 0.356 Chirality : 0.046 0.182 6420 Planarity : 0.005 0.055 7461 Dihedral : 5.683 101.193 6290 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 4.66 % Allowed : 15.20 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: -0.25 (0.11), residues: 5794 helix: 1.36 (0.09), residues: 3232 sheet: -1.76 (0.20), residues: 609 loop : -2.29 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 74 TYR 0.019 0.002 TYR D 286 PHE 0.018 0.002 PHE C 205 TRP 0.014 0.002 TRP A 330 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00585 (40722) covalent geometry : angle 0.69937 (55363) hydrogen bonds : bond 0.04237 ( 2696) hydrogen bonds : angle 4.62031 ( 7932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 611 time to evaluate : 1.371 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 85 ASP cc_start: 0.8480 (p0) cc_final: 0.8235 (p0) REVERT: A 325 ASP cc_start: 0.8455 (t70) cc_final: 0.8239 (t0) REVERT: A 504 ASP cc_start: 0.7982 (t70) cc_final: 0.7661 (t70) REVERT: A 568 LYS cc_start: 0.8711 (mptm) cc_final: 0.8359 (pttp) REVERT: B 40 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 81 ASN cc_start: 0.8388 (t0) cc_final: 0.7971 (t0) REVERT: B 153 VAL cc_start: 0.8967 (t) cc_final: 0.8755 (t) REVERT: B 456 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 460 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7514 (ttp-110) REVERT: B 492 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7869 (mt-10) REVERT: B 506 TYR cc_start: 0.7962 (t80) cc_final: 0.7747 (t80) REVERT: C 41 ARG cc_start: 0.8261 (tmm-80) cc_final: 0.7717 (ttt180) REVERT: C 491 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: C 520 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8975 (mm) REVERT: C 530 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9067 (tt) REVERT: D 49 GLU cc_start: 0.7878 (tt0) cc_final: 0.7319 (tm-30) REVERT: D 149 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8297 (pmmt) REVERT: D 342 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 393 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7934 (ptp-170) REVERT: F 94 ASN cc_start: 0.8177 (p0) cc_final: 0.7867 (p0) REVERT: F 177 LEU cc_start: 0.7771 (mm) cc_final: 0.7485 (mm) REVERT: F 315 SER cc_start: 0.8869 (m) cc_final: 0.8281 (p) REVERT: F 329 THR cc_start: 0.9439 (m) cc_final: 0.9210 (m) REVERT: G 50 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7967 (mtt-85) REVERT: G 61 TYR cc_start: 0.7965 (m-80) cc_final: 0.7619 (m-80) REVERT: G 125 GLU cc_start: 0.8489 (tp30) cc_final: 0.8052 (tp30) REVERT: G 186 ARG cc_start: 0.8835 (tpp80) cc_final: 0.8634 (mpp80) REVERT: G 208 GLU cc_start: 0.7125 (tp30) cc_final: 0.6879 (tt0) REVERT: H 9 THR cc_start: 0.7148 (m) cc_final: 0.6738 (p) REVERT: H 19 GLU cc_start: 0.8107 (tp30) cc_final: 0.7740 (tp30) REVERT: H 21 TYR cc_start: 0.8326 (m-10) cc_final: 0.7963 (m-10) REVERT: H 51 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8198 (mp) REVERT: H 54 ASP cc_start: 0.7578 (p0) cc_final: 0.7205 (p0) REVERT: H 61 ARG cc_start: 0.7821 (tmt-80) cc_final: 0.7272 (ttp-110) REVERT: H 87 GLU cc_start: 0.8323 (mp0) cc_final: 0.7738 (mm-30) REVERT: J 58 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7031 (tmm-80) REVERT: J 107 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7597 (pp) REVERT: J 112 LEU cc_start: 0.8144 (mp) cc_final: 0.7859 (tp) REVERT: K 22 LEU cc_start: 0.0257 (OUTLIER) cc_final: -0.0038 (mm) REVERT: K 45 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7340 (tm-30) REVERT: L 82 GLU cc_start: 0.8260 (tp30) cc_final: 0.7862 (tp30) outliers start: 151 outliers final: 107 residues processed: 722 average time/residue: 0.2754 time to fit residues: 310.4294 Evaluate side-chains 686 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 571 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 429 ASN Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 77 GLU Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 140 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 503 optimal weight: 10.0000 chunk 416 optimal weight: 50.0000 chunk 233 optimal weight: 6.9990 chunk 299 optimal weight: 0.0070 chunk 523 optimal weight: 50.0000 chunk 407 optimal weight: 0.0470 chunk 406 optimal weight: 40.0000 chunk 519 optimal weight: 40.0000 overall best weight: 5.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN A 465 GLN A 571 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098786 restraints weight = 75240.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101727 restraints weight = 37211.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102700 restraints weight = 21844.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103854 restraints weight = 16175.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104513 restraints weight = 12131.300| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40722 Z= 0.195 Angle : 0.655 17.474 55363 Z= 0.332 Chirality : 0.044 0.170 6420 Planarity : 0.004 0.050 7461 Dihedral : 5.439 76.031 6290 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 4.35 % Allowed : 16.22 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.08 (0.11), residues: 5794 helix: 1.64 (0.09), residues: 3238 sheet: -1.71 (0.21), residues: 592 loop : -2.15 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 74 TYR 0.023 0.001 TYR D 13 PHE 0.016 0.001 PHE G 130 TRP 0.012 0.001 TRP A 424 HIS 0.004 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00445 (40722) covalent geometry : angle 0.65544 (55363) hydrogen bonds : bond 0.03998 ( 2696) hydrogen bonds : angle 4.47736 ( 7932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 629 time to evaluate : 1.494 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 85 ASP cc_start: 0.8436 (p0) cc_final: 0.8167 (p0) REVERT: A 238 GLN cc_start: 0.8575 (mt0) cc_final: 0.8174 (mt0) REVERT: A 325 ASP cc_start: 0.8419 (t70) cc_final: 0.8211 (t0) REVERT: A 504 ASP cc_start: 0.7998 (t70) cc_final: 0.7660 (t70) REVERT: A 568 LYS cc_start: 0.8716 (mptm) cc_final: 0.8348 (pttp) REVERT: B 40 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 81 ASN cc_start: 0.8284 (t0) cc_final: 0.7892 (t0) REVERT: B 153 VAL cc_start: 0.8940 (t) cc_final: 0.8702 (t) REVERT: B 294 MET cc_start: 0.8942 (mmm) cc_final: 0.8317 (mtt) REVERT: B 456 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7335 (tm-30) REVERT: B 460 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7473 (ttp-110) REVERT: C 41 ARG cc_start: 0.8175 (tmm-80) cc_final: 0.7646 (ttt180) REVERT: C 491 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: C 520 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8971 (mm) REVERT: D 49 GLU cc_start: 0.7784 (tt0) cc_final: 0.7267 (tm-30) REVERT: D 167 ILE cc_start: 0.9213 (pt) cc_final: 0.8922 (mt) REVERT: D 287 MET cc_start: 0.8593 (ttm) cc_final: 0.7957 (ttp) REVERT: D 342 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8086 (tm-30) REVERT: F 94 ASN cc_start: 0.8179 (p0) cc_final: 0.7883 (p0) REVERT: F 236 ARG cc_start: 0.8790 (mmt-90) cc_final: 0.8527 (mmt-90) REVERT: F 315 SER cc_start: 0.8835 (m) cc_final: 0.8221 (p) REVERT: F 329 THR cc_start: 0.9412 (m) cc_final: 0.9156 (m) REVERT: G 19 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7810 (mtm110) REVERT: G 61 TYR cc_start: 0.7968 (m-80) cc_final: 0.7664 (m-80) REVERT: G 125 GLU cc_start: 0.8387 (tp30) cc_final: 0.7971 (tp30) REVERT: G 208 GLU cc_start: 0.7105 (tp30) cc_final: 0.6791 (tt0) REVERT: H 4 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8306 (pp) REVERT: H 9 THR cc_start: 0.7052 (m) cc_final: 0.6665 (p) REVERT: H 19 GLU cc_start: 0.8123 (tp30) cc_final: 0.7594 (tp30) REVERT: H 21 TYR cc_start: 0.8351 (m-10) cc_final: 0.7859 (m-10) REVERT: H 54 ASP cc_start: 0.7411 (p0) cc_final: 0.6941 (p0) REVERT: H 61 ARG cc_start: 0.7835 (tmt-80) cc_final: 0.7273 (ttp-110) REVERT: H 87 GLU cc_start: 0.8306 (mp0) cc_final: 0.7933 (mm-30) REVERT: J 58 ARG cc_start: 0.8198 (mtm180) cc_final: 0.6965 (tmm-80) REVERT: J 107 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7577 (pp) REVERT: J 112 LEU cc_start: 0.8115 (mp) cc_final: 0.7839 (tp) REVERT: K 22 LEU cc_start: 0.0464 (OUTLIER) cc_final: 0.0134 (mm) REVERT: K 45 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7370 (tm-30) REVERT: L 82 GLU cc_start: 0.8248 (tp30) cc_final: 0.7915 (tp30) outliers start: 141 outliers final: 100 residues processed: 732 average time/residue: 0.2774 time to fit residues: 317.6698 Evaluate side-chains 687 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 582 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 24 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 376 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 chunk 394 optimal weight: 0.0270 chunk 167 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN G 185 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098779 restraints weight = 75515.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102002 restraints weight = 37456.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102691 restraints weight = 22158.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103839 restraints weight = 16207.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104748 restraints weight = 12044.441| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40722 Z= 0.190 Angle : 0.658 17.656 55363 Z= 0.332 Chirality : 0.044 0.172 6420 Planarity : 0.005 0.109 7461 Dihedral : 5.327 65.003 6290 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.02 % Favored : 93.96 % Rotamer: Outliers : 4.87 % Allowed : 16.99 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.29 (0.12), residues: 5794 helix: 1.82 (0.09), residues: 3238 sheet: -1.63 (0.21), residues: 572 loop : -2.07 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 74 TYR 0.023 0.001 TYR C 353 PHE 0.016 0.001 PHE G 130 TRP 0.011 0.001 TRP C 330 HIS 0.004 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00438 (40722) covalent geometry : angle 0.65824 (55363) hydrogen bonds : bond 0.03910 ( 2696) hydrogen bonds : angle 4.40737 ( 7932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 633 time to evaluate : 1.402 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 85 ASP cc_start: 0.8406 (p0) cc_final: 0.8149 (p0) REVERT: A 184 TYR cc_start: 0.9142 (p90) cc_final: 0.8875 (p90) REVERT: A 238 GLN cc_start: 0.8605 (mt0) cc_final: 0.8236 (mt0) REVERT: A 422 ILE cc_start: 0.9565 (mp) cc_final: 0.9356 (mp) REVERT: A 504 ASP cc_start: 0.7993 (t70) cc_final: 0.7695 (t70) REVERT: A 568 LYS cc_start: 0.8694 (mptm) cc_final: 0.8345 (pttp) REVERT: B 40 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 81 ASN cc_start: 0.8340 (t0) cc_final: 0.7938 (t0) REVERT: B 153 VAL cc_start: 0.8921 (t) cc_final: 0.8678 (t) REVERT: B 294 MET cc_start: 0.8932 (mmm) cc_final: 0.8375 (mtt) REVERT: B 456 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7468 (tm-30) REVERT: C 1 MET cc_start: 0.7217 (tmm) cc_final: 0.6919 (tmm) REVERT: C 41 ARG cc_start: 0.8161 (tmm-80) cc_final: 0.7606 (ttt180) REVERT: C 491 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7896 (mtm-85) REVERT: C 520 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8966 (mm) REVERT: C 530 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9165 (tt) REVERT: D 49 GLU cc_start: 0.7738 (tt0) cc_final: 0.7203 (tm-30) REVERT: D 149 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8221 (pmmt) REVERT: D 254 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9045 (tp) REVERT: D 342 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8114 (tm-30) REVERT: E 237 MET cc_start: 0.8126 (mmm) cc_final: 0.7711 (mtt) REVERT: F 94 ASN cc_start: 0.8148 (p0) cc_final: 0.7895 (p0) REVERT: F 315 SER cc_start: 0.8822 (m) cc_final: 0.8217 (p) REVERT: F 329 THR cc_start: 0.9351 (m) cc_final: 0.9131 (m) REVERT: G 19 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7793 (mtm110) REVERT: G 61 TYR cc_start: 0.7964 (m-80) cc_final: 0.7657 (m-80) REVERT: G 125 GLU cc_start: 0.8361 (tp30) cc_final: 0.7959 (tp30) REVERT: G 186 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7221 (mpp80) REVERT: H 4 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8357 (pp) REVERT: H 9 THR cc_start: 0.7116 (m) cc_final: 0.6708 (p) REVERT: H 19 GLU cc_start: 0.8093 (tp30) cc_final: 0.7486 (tp30) REVERT: H 21 TYR cc_start: 0.8372 (m-10) cc_final: 0.7871 (m-10) REVERT: H 51 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8212 (mp) REVERT: H 54 ASP cc_start: 0.7228 (p0) cc_final: 0.6704 (p0) REVERT: H 61 ARG cc_start: 0.7771 (tmt-80) cc_final: 0.7283 (ttp-110) REVERT: H 87 GLU cc_start: 0.8273 (mp0) cc_final: 0.7946 (mm-30) REVERT: J 58 ARG cc_start: 0.8210 (mtm180) cc_final: 0.6958 (tmm-80) REVERT: J 97 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7656 (mtmm) REVERT: J 107 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7637 (pp) REVERT: K 22 LEU cc_start: 0.0593 (OUTLIER) cc_final: 0.0305 (mm) REVERT: K 45 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7401 (tm-30) REVERT: L 82 GLU cc_start: 0.8218 (tp30) cc_final: 0.7909 (tp30) outliers start: 158 outliers final: 119 residues processed: 747 average time/residue: 0.2666 time to fit residues: 311.7814 Evaluate side-chains 713 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 584 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 231 optimal weight: 6.9990 chunk 408 optimal weight: 30.0000 chunk 362 optimal weight: 40.0000 chunk 450 optimal weight: 50.0000 chunk 121 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 549 optimal weight: 50.0000 chunk 378 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 167 optimal weight: 0.0270 chunk 392 optimal weight: 2.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN G 22 GLN G 185 GLN K 32 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099359 restraints weight = 75262.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102291 restraints weight = 38079.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103058 restraints weight = 23436.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104424 restraints weight = 16541.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105063 restraints weight = 12124.229| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40722 Z= 0.177 Angle : 0.652 16.722 55363 Z= 0.330 Chirality : 0.044 0.231 6420 Planarity : 0.005 0.060 7461 Dihedral : 5.216 60.367 6290 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.92 % Favored : 94.06 % Rotamer: Outliers : 4.44 % Allowed : 18.10 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.43 (0.12), residues: 5794 helix: 1.92 (0.09), residues: 3246 sheet: -1.57 (0.22), residues: 542 loop : -1.99 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 74 TYR 0.025 0.001 TYR I 73 PHE 0.015 0.001 PHE C 406 TRP 0.012 0.001 TRP J 100 HIS 0.003 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00403 (40722) covalent geometry : angle 0.65245 (55363) hydrogen bonds : bond 0.03838 ( 2696) hydrogen bonds : angle 4.35008 ( 7932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 625 time to evaluate : 1.515 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 85 ASP cc_start: 0.8389 (p0) cc_final: 0.8131 (p0) REVERT: A 238 GLN cc_start: 0.8607 (mt0) cc_final: 0.8261 (mt0) REVERT: A 504 ASP cc_start: 0.7996 (t70) cc_final: 0.7682 (t70) REVERT: A 568 LYS cc_start: 0.8684 (mptm) cc_final: 0.8352 (pttp) REVERT: B 25 TYR cc_start: 0.7888 (m-80) cc_final: 0.7267 (m-80) REVERT: B 40 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 81 ASN cc_start: 0.8267 (t0) cc_final: 0.7856 (t0) REVERT: B 153 VAL cc_start: 0.8887 (t) cc_final: 0.8638 (t) REVERT: B 294 MET cc_start: 0.8921 (mmm) cc_final: 0.8337 (mtt) REVERT: B 456 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7360 (tm-30) REVERT: B 460 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: B 476 LEU cc_start: 0.8617 (mm) cc_final: 0.8264 (pp) REVERT: B 481 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7920 (tmm-80) REVERT: C 1 MET cc_start: 0.7235 (tmm) cc_final: 0.6886 (tmm) REVERT: C 41 ARG cc_start: 0.8175 (tmm-80) cc_final: 0.7611 (ttt180) REVERT: C 491 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: C 520 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 530 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9130 (tt) REVERT: D 49 GLU cc_start: 0.7700 (tt0) cc_final: 0.7182 (tm-30) REVERT: D 149 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8219 (pmmt) REVERT: D 254 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9048 (tp) REVERT: D 342 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8073 (tm-30) REVERT: F 94 ASN cc_start: 0.8201 (p0) cc_final: 0.7931 (p0) REVERT: F 236 ARG cc_start: 0.8768 (mmt-90) cc_final: 0.8460 (mmt-90) REVERT: F 315 SER cc_start: 0.8832 (m) cc_final: 0.8224 (p) REVERT: G 19 ARG cc_start: 0.8185 (mtm110) cc_final: 0.7852 (mtm-85) REVERT: G 61 TYR cc_start: 0.8087 (m-80) cc_final: 0.7791 (m-80) REVERT: G 125 GLU cc_start: 0.8371 (tp30) cc_final: 0.7965 (tp30) REVERT: G 186 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7337 (mpp80) REVERT: H 4 ILE cc_start: 0.8645 (pp) cc_final: 0.8356 (pp) REVERT: H 9 THR cc_start: 0.7107 (m) cc_final: 0.6720 (p) REVERT: H 19 GLU cc_start: 0.8149 (tp30) cc_final: 0.7455 (tp30) REVERT: H 21 TYR cc_start: 0.8382 (m-10) cc_final: 0.7883 (m-10) REVERT: H 51 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8193 (mp) REVERT: H 54 ASP cc_start: 0.7057 (p0) cc_final: 0.6173 (p0) REVERT: H 61 ARG cc_start: 0.7817 (tmt-80) cc_final: 0.7348 (ttp80) REVERT: H 87 GLU cc_start: 0.8246 (mp0) cc_final: 0.7926 (mm-30) REVERT: J 58 ARG cc_start: 0.8292 (mtm180) cc_final: 0.7024 (tmm-80) REVERT: J 97 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7784 (mtmm) REVERT: J 107 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7660 (pp) REVERT: J 121 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7686 (mp) REVERT: J 172 ASP cc_start: 0.8378 (m-30) cc_final: 0.8177 (m-30) REVERT: K 22 LEU cc_start: 0.0817 (OUTLIER) cc_final: 0.0516 (mm) REVERT: K 45 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7427 (tm-30) REVERT: L 82 GLU cc_start: 0.8205 (tp30) cc_final: 0.7921 (tp30) outliers start: 144 outliers final: 115 residues processed: 727 average time/residue: 0.2701 time to fit residues: 307.4442 Evaluate side-chains 709 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 584 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 532 optimal weight: 50.0000 chunk 332 optimal weight: 0.9980 chunk 283 optimal weight: 10.0000 chunk 422 optimal weight: 50.0000 chunk 305 optimal weight: 10.0000 chunk 460 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 476 optimal weight: 50.0000 chunk 293 optimal weight: 6.9990 chunk 463 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN G 22 GLN G 185 GLN J 52 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098926 restraints weight = 74670.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102095 restraints weight = 38013.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103023 restraints weight = 23159.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.104253 restraints weight = 16768.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105566 restraints weight = 12282.851| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40722 Z= 0.205 Angle : 0.674 17.304 55363 Z= 0.342 Chirality : 0.045 0.214 6420 Planarity : 0.005 0.071 7461 Dihedral : 5.197 57.656 6290 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.99 % Favored : 93.99 % Rotamer: Outliers : 4.66 % Allowed : 18.13 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.51 (0.12), residues: 5794 helix: 1.97 (0.09), residues: 3248 sheet: -1.55 (0.22), residues: 542 loop : -1.94 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 78 TYR 0.023 0.001 TYR I 73 PHE 0.016 0.001 PHE G 130 TRP 0.012 0.001 TRP C 330 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00475 (40722) covalent geometry : angle 0.67366 (55363) hydrogen bonds : bond 0.03861 ( 2696) hydrogen bonds : angle 4.34979 ( 7932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 604 time to evaluate : 1.479 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 85 ASP cc_start: 0.8381 (p0) cc_final: 0.8126 (p0) REVERT: A 238 GLN cc_start: 0.8623 (mt0) cc_final: 0.8272 (mt0) REVERT: A 300 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8451 (tm-30) REVERT: A 504 ASP cc_start: 0.7988 (t70) cc_final: 0.7690 (t70) REVERT: A 568 LYS cc_start: 0.8656 (mptm) cc_final: 0.8374 (pttp) REVERT: B 40 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8433 (mt) REVERT: B 81 ASN cc_start: 0.8262 (t0) cc_final: 0.7845 (t0) REVERT: B 153 VAL cc_start: 0.8879 (t) cc_final: 0.8592 (t) REVERT: B 294 MET cc_start: 0.8907 (mmm) cc_final: 0.8351 (mtt) REVERT: B 456 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7318 (tm-30) REVERT: B 460 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7410 (ttm-80) REVERT: B 476 LEU cc_start: 0.8703 (mm) cc_final: 0.8301 (pp) REVERT: C 1 MET cc_start: 0.7177 (tmm) cc_final: 0.6891 (tmm) REVERT: C 41 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7660 (ttt180) REVERT: C 342 GLU cc_start: 0.7536 (pm20) cc_final: 0.7314 (pm20) REVERT: C 491 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: C 520 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8975 (mm) REVERT: C 530 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9103 (tt) REVERT: D 149 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8278 (pmmt) REVERT: D 342 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 409 ARG cc_start: 0.7626 (mmt180) cc_final: 0.6725 (mmt180) REVERT: E 452 LYS cc_start: 0.8316 (ptpp) cc_final: 0.8115 (ptpp) REVERT: F 94 ASN cc_start: 0.8220 (p0) cc_final: 0.7952 (p0) REVERT: F 315 SER cc_start: 0.8829 (m) cc_final: 0.8222 (p) REVERT: G 19 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7844 (mtm110) REVERT: G 125 GLU cc_start: 0.8365 (tp30) cc_final: 0.7968 (tp30) REVERT: G 186 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7481 (mpp80) REVERT: H 4 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8400 (pp) REVERT: H 9 THR cc_start: 0.7150 (m) cc_final: 0.6932 (p) REVERT: H 19 GLU cc_start: 0.8182 (tp30) cc_final: 0.7452 (tp30) REVERT: H 21 TYR cc_start: 0.8394 (m-10) cc_final: 0.7902 (m-10) REVERT: H 51 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (mp) REVERT: H 61 ARG cc_start: 0.7890 (tmt-80) cc_final: 0.7476 (ttp80) REVERT: H 87 GLU cc_start: 0.8207 (mp0) cc_final: 0.7890 (mm-30) REVERT: I 73 TYR cc_start: 0.5209 (t80) cc_final: 0.4943 (t80) REVERT: J 58 ARG cc_start: 0.8291 (mtm180) cc_final: 0.6997 (tmm-80) REVERT: J 97 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7721 (mtmm) REVERT: J 107 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (pp) REVERT: J 178 LEU cc_start: 0.8638 (mt) cc_final: 0.8422 (mt) REVERT: K 22 LEU cc_start: 0.0915 (OUTLIER) cc_final: 0.0612 (mm) REVERT: K 45 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7345 (tm-30) REVERT: L 82 GLU cc_start: 0.8187 (tp30) cc_final: 0.7916 (tp30) REVERT: L 141 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6351 (pm20) outliers start: 151 outliers final: 125 residues processed: 715 average time/residue: 0.2805 time to fit residues: 313.7939 Evaluate side-chains 709 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 574 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 508 optimal weight: 50.0000 chunk 567 optimal weight: 40.0000 chunk 305 optimal weight: 8.9990 chunk 393 optimal weight: 20.0000 chunk 513 optimal weight: 20.0000 chunk 311 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 524 optimal weight: 40.0000 chunk 560 optimal weight: 40.0000 chunk 537 optimal weight: 50.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN J 52 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096555 restraints weight = 75807.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099458 restraints weight = 39464.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.100429 restraints weight = 24551.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101793 restraints weight = 17371.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103038 restraints weight = 12532.961| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 40722 Z= 0.307 Angle : 0.759 19.263 55363 Z= 0.386 Chirality : 0.048 0.249 6420 Planarity : 0.005 0.077 7461 Dihedral : 5.405 56.100 6290 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.90 % Favored : 93.08 % Rotamer: Outliers : 4.81 % Allowed : 18.41 % Favored : 76.78 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.43 (0.12), residues: 5794 helix: 1.94 (0.09), residues: 3233 sheet: -1.64 (0.21), residues: 557 loop : -1.98 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 547 TYR 0.020 0.002 TYR C 353 PHE 0.025 0.002 PHE G 130 TRP 0.016 0.002 TRP C 330 HIS 0.007 0.002 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00717 (40722) covalent geometry : angle 0.75948 (55363) hydrogen bonds : bond 0.04198 ( 2696) hydrogen bonds : angle 4.48297 ( 7932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 581 time to evaluate : 1.505 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: A 85 ASP cc_start: 0.8412 (p0) cc_final: 0.8192 (p0) REVERT: A 238 GLN cc_start: 0.8654 (mt0) cc_final: 0.8321 (mt0) REVERT: A 466 GLU cc_start: 0.7268 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 504 ASP cc_start: 0.8016 (t70) cc_final: 0.7725 (t70) REVERT: A 568 LYS cc_start: 0.8691 (mptm) cc_final: 0.8381 (pttp) REVERT: B 153 VAL cc_start: 0.8890 (t) cc_final: 0.8689 (t) REVERT: B 294 MET cc_start: 0.8947 (mmm) cc_final: 0.8478 (mtt) REVERT: B 456 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 1 MET cc_start: 0.7178 (tmm) cc_final: 0.6890 (tmm) REVERT: C 41 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.7722 (tmm-80) REVERT: C 491 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: C 520 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8971 (mm) REVERT: D 36 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7696 (ttpt) REVERT: D 49 GLU cc_start: 0.7769 (tt0) cc_final: 0.7346 (tm-30) REVERT: D 342 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8142 (tm-30) REVERT: E 445 MET cc_start: 0.8580 (mtm) cc_final: 0.8354 (mtm) REVERT: F 94 ASN cc_start: 0.8250 (p0) cc_final: 0.7993 (p0) REVERT: F 315 SER cc_start: 0.8854 (m) cc_final: 0.8266 (p) REVERT: G 19 ARG cc_start: 0.8154 (mtm110) cc_final: 0.7887 (mtm110) REVERT: G 125 GLU cc_start: 0.8365 (tp30) cc_final: 0.7973 (tp30) REVERT: G 177 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: G 186 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7559 (mpp80) REVERT: H 9 THR cc_start: 0.7349 (m) cc_final: 0.6826 (p) REVERT: H 39 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7416 (tpm170) REVERT: H 51 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8167 (mp) REVERT: H 61 ARG cc_start: 0.7813 (tmt-80) cc_final: 0.7421 (ttp80) REVERT: H 78 LYS cc_start: 0.7082 (mmtt) cc_final: 0.6795 (mmtt) REVERT: H 87 GLU cc_start: 0.8196 (mp0) cc_final: 0.7905 (mm-30) REVERT: J 58 ARG cc_start: 0.8400 (mtm180) cc_final: 0.7064 (tmm-80) REVERT: J 107 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7857 (pp) REVERT: J 178 LEU cc_start: 0.8752 (mt) cc_final: 0.8550 (mt) REVERT: K 22 LEU cc_start: 0.0597 (OUTLIER) cc_final: 0.0330 (mm) REVERT: K 45 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7380 (tm-30) REVERT: K 65 LYS cc_start: 0.4877 (ptpp) cc_final: 0.4494 (ptpp) REVERT: L 82 GLU cc_start: 0.8228 (tp30) cc_final: 0.7817 (tp30) REVERT: L 85 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8025 (ttp-110) REVERT: L 141 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6287 (pm20) outliers start: 156 outliers final: 131 residues processed: 697 average time/residue: 0.2797 time to fit residues: 305.0169 Evaluate side-chains 692 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 553 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain B residue 28 CYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 516 MET Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 296 GLU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 194 MET Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 112 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 480 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 471 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 302 optimal weight: 7.9990 chunk 429 optimal weight: 0.0010 chunk 63 optimal weight: 0.9980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 185 GLN J 52 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103291 restraints weight = 74242.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105806 restraints weight = 37001.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106740 restraints weight = 22351.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107835 restraints weight = 15721.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108066 restraints weight = 12298.870| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40722 Z= 0.133 Angle : 0.664 17.515 55363 Z= 0.336 Chirality : 0.043 0.242 6420 Planarity : 0.004 0.081 7461 Dihedral : 5.092 53.449 6288 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.95 % Favored : 95.03 % Rotamer: Outliers : 2.96 % Allowed : 20.35 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.71 (0.12), residues: 5794 helix: 2.11 (0.09), residues: 3254 sheet: -1.47 (0.21), residues: 591 loop : -1.81 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 105 TYR 0.039 0.001 TYR C 353 PHE 0.013 0.001 PHE A 406 TRP 0.014 0.001 TRP J 100 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00285 (40722) covalent geometry : angle 0.66418 (55363) hydrogen bonds : bond 0.03661 ( 2696) hydrogen bonds : angle 4.27748 ( 7932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11588 Ramachandran restraints generated. 5794 Oldfield, 0 Emsley, 5794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 630 time to evaluate : 1.601 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 85 ASP cc_start: 0.8341 (p0) cc_final: 0.7993 (p0) REVERT: A 234 LYS cc_start: 0.8891 (tppp) cc_final: 0.8424 (tttm) REVERT: A 238 GLN cc_start: 0.8556 (mt0) cc_final: 0.8269 (mt0) REVERT: A 300 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8371 (tm-30) REVERT: A 424 TRP cc_start: 0.8053 (p90) cc_final: 0.7699 (p90) REVERT: A 504 ASP cc_start: 0.7900 (t70) cc_final: 0.7623 (t70) REVERT: A 568 LYS cc_start: 0.8642 (mptm) cc_final: 0.8330 (pttp) REVERT: B 25 TYR cc_start: 0.7827 (m-80) cc_final: 0.7189 (m-80) REVERT: B 153 VAL cc_start: 0.8794 (t) cc_final: 0.8560 (t) REVERT: B 456 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7391 (tm-30) REVERT: B 460 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7388 (ttp-110) REVERT: B 476 LEU cc_start: 0.8448 (mp) cc_final: 0.8040 (pp) REVERT: B 493 ASP cc_start: 0.7529 (m-30) cc_final: 0.7210 (t0) REVERT: C 1 MET cc_start: 0.7290 (tmm) cc_final: 0.7033 (tmm) REVERT: C 41 ARG cc_start: 0.8115 (tmm-80) cc_final: 0.7770 (tmm-80) REVERT: C 85 ASP cc_start: 0.8355 (p0) cc_final: 0.8150 (p0) REVERT: C 491 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7653 (mtm180) REVERT: C 520 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8926 (mm) REVERT: C 530 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9060 (tt) REVERT: D 36 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7661 (ttpt) REVERT: D 342 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 223 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8202 (mppt) REVERT: E 290 ASP cc_start: 0.8210 (m-30) cc_final: 0.8004 (m-30) REVERT: E 318 ASP cc_start: 0.8040 (t0) cc_final: 0.7646 (t0) REVERT: F 94 ASN cc_start: 0.7996 (p0) cc_final: 0.7687 (p0) REVERT: F 315 SER cc_start: 0.8788 (m) cc_final: 0.8192 (p) REVERT: G 19 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7916 (mtm-85) REVERT: G 125 GLU cc_start: 0.8380 (tp30) cc_final: 0.7985 (tp30) REVERT: G 186 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7420 (mpp80) REVERT: H 4 ILE cc_start: 0.8540 (pp) cc_final: 0.8260 (pp) REVERT: H 11 GLN cc_start: 0.7211 (pp30) cc_final: 0.6839 (pt0) REVERT: H 19 GLU cc_start: 0.7926 (tp30) cc_final: 0.7416 (tt0) REVERT: H 51 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8115 (mp) REVERT: H 61 ARG cc_start: 0.7799 (tmt-80) cc_final: 0.7430 (ttp80) REVERT: H 87 GLU cc_start: 0.8343 (mp0) cc_final: 0.8064 (mm-30) REVERT: J 58 ARG cc_start: 0.8236 (mtm180) cc_final: 0.7032 (tmm-80) REVERT: J 107 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7486 (pp) REVERT: J 172 ASP cc_start: 0.8383 (m-30) cc_final: 0.8116 (m-30) REVERT: K 65 LYS cc_start: 0.4796 (ptpp) cc_final: 0.4462 (ptpp) REVERT: L 82 GLU cc_start: 0.8268 (tp30) cc_final: 0.7996 (tp30) REVERT: L 141 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5884 (pm20) outliers start: 96 outliers final: 75 residues processed: 698 average time/residue: 0.2860 time to fit residues: 310.3027 Evaluate side-chains 668 residues out of total 4580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 586 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 108 PHE Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 186 ARG Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 41 LEU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 85 ARG Chi-restraints excluded: chain L residue 100 TRP Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 574 random chunks: chunk 557 optimal weight: 50.0000 chunk 299 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 411 optimal weight: 40.0000 chunk 514 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 343 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** G 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 GLN ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099506 restraints weight = 75138.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102576 restraints weight = 37997.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103572 restraints weight = 23487.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104908 restraints weight = 16806.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106068 restraints weight = 12153.348| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40722 Z= 0.189 Angle : 0.692 17.883 55363 Z= 0.349 Chirality : 0.045 0.253 6420 Planarity : 0.005 0.075 7461 Dihedral : 5.069 55.922 6288 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.83 % Favored : 94.15 % Rotamer: Outliers : 3.18 % Allowed : 20.88 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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 are not related in a simple way. whole: 0.75 (0.12), residues: 5794 helix: 2.13 (0.09), residues: 3256 sheet: -1.41 (0.22), residues: 552 loop : -1.79 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 74 TYR 0.033 0.002 TYR I 73 PHE 0.018 0.001 PHE F 20 TRP 0.015 0.001 TRP A 330 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.00438 (40722) covalent geometry : angle 0.69193 (55363) hydrogen bonds : bond 0.03755 ( 2696) hydrogen bonds : angle 4.26664 ( 7932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8240.12 seconds wall clock time: 142 minutes 17.77 seconds (8537.77 seconds total)