Starting phenix.real_space_refine on Mon Jul 6 11:18:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.map" model { file = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lmz_23443/07_2026/7lmz_23443.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 32 5.49 5 Mg 8 5.21 5 S 178 5.16 5 C 21908 2.51 5 N 6212 2.21 5 O 6656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34994 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5800 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 661} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.38, per 1000 atoms: 0.24 Number of scatterers: 34994 At special positions: 0 Unit cell: (163.702, 171.143, 135.001, 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 178 16.00 P 32 15.00 Mg 8 11.99 O 6656 8.00 N 6212 7.00 C 21908 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: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8290 Finding SS restraints... Secondary structure from input PDB file: 211 helices and 33 sheets defined 52.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.750A pdb=" N GLU A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.505A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.927A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.527A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 4.143A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.800A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.790A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.987A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.594A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.226A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.288A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.905A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 removed outlier: 3.546A pdb=" N SER A 612 " --> pdb=" O MET A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.610A pdb=" N LEU A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.579A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 714 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 748 through 766 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.577A pdb=" N GLU B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.562A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.017A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.629A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.784A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.751A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.707A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 548 removed outlier: 4.518A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 579 through 582 Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.575A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.661A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.527A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 removed outlier: 4.484A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.696A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.157A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.129A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.788A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.638A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.720A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 430 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 465 removed outlier: 3.591A pdb=" N ARG C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.778A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.842A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 714 Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.597A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 Processing helix chain 'D' and resid 12 through 17 removed outlier: 4.359A pdb=" N ILE D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.652A pdb=" N GLU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 233 removed outlier: 4.369A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.530A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.208A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.509A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 373 through 386 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 548 removed outlier: 3.817A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 548 " --> pdb=" O PRO D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 569 Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.248A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 4.029A pdb=" N GLY D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 Processing helix chain 'D' and resid 732 through 742 Processing helix chain 'D' and resid 748 through 767 removed outlier: 3.684A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.079A pdb=" N ARG E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.751A pdb=" N GLU E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.868A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 272 through 275 Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.253A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 335 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.699A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.616A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.510A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.703A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 462 through 466 removed outlier: 4.352A pdb=" N GLU E 466 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.763A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 553 through 569 removed outlier: 3.561A pdb=" N ALA E 557 " --> pdb=" O GLY E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 587 through 592 removed outlier: 3.989A pdb=" N GLY E 591 " --> pdb=" O GLY E 587 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP E 592 " --> pdb=" O GLY E 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 587 through 592' Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.704A pdb=" N ARG E 599 " --> pdb=" O GLY E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.831A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 741 Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.526A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.574A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 199 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.157A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.037A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.824A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 removed outlier: 3.529A pdb=" N LYS F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.827A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.541A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.902A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 4.199A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 612 Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.862A pdb=" N LEU F 634 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 664 removed outlier: 4.183A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER F 664 " --> pdb=" O ASN F 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.637A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 removed outlier: 3.513A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.714A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.620A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 177 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG A 113 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N ASP A 179 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 11.521A pdb=" N HIS A 115 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N VAL A 181 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 11.203A pdb=" N LEU A 117 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N HIS A 183 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.492A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.320A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 84 removed outlier: 6.209A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 70 Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.825A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA9, first strand: chain 'B' and resid 268 through 270 removed outlier: 5.997A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.555A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.590A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.542A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.828A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.632A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.568A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 5.724A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 65 through 70 removed outlier: 3.697A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 109 through 110 removed outlier: 7.674A pdb=" N LYS D 109 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.633A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.390A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.610A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.693A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.859A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.766A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.379A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 543 removed outlier: 6.502A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.389A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 38 through 41 removed outlier: 3.566A pdb=" N ARG F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 113 through 115 removed outlier: 3.738A pdb=" N ILE F 114 " --> pdb=" O VAL F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 117 through 118 Processing sheet with id=AD4, first strand: chain 'F' and resid 146 through 147 removed outlier: 3.593A pdb=" N ILE F 146 " --> pdb=" O CYS F 174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 266 through 270 removed outlier: 3.507A pdb=" N PHE F 267 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 538 through 542 removed outlier: 5.992A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) 1617 hydrogen bonds defined for protein. 4662 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: 8.29 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11941 1.34 - 1.46: 5692 1.46 - 1.58: 17620 1.58 - 1.70: 39 1.70 - 1.82: 284 Bond restraints: 35576 Sorted by residual: bond pdb=" CB PRO A 246 " pdb=" CG PRO A 246 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO B 372 " pdb=" CG PRO B 372 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.94e+00 bond pdb=" CB PRO B 729 " pdb=" CG PRO B 729 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.64e+00 bond pdb=" N ASP E 169 " pdb=" CA ASP E 169 " ideal model delta sigma weight residual 1.462 1.445 0.017 1.05e-02 9.07e+03 2.52e+00 bond pdb=" CG PRO B 729 " pdb=" CD PRO B 729 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.28e+00 ... (remaining 35571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 47449 2.32 - 4.65: 571 4.65 - 6.97: 72 6.97 - 9.30: 9 9.30 - 11.62: 1 Bond angle restraints: 48102 Sorted by residual: angle pdb=" CA PRO A 246 " pdb=" N PRO A 246 " pdb=" CD PRO A 246 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.28e+01 angle pdb=" CA PRO B 729 " pdb=" N PRO B 729 " pdb=" CD PRO B 729 " ideal model delta sigma weight residual 112.00 104.50 7.50 1.40e+00 5.10e-01 2.87e+01 angle pdb=" CA PRO B 372 " pdb=" N PRO B 372 " pdb=" CD PRO B 372 " ideal model delta sigma weight residual 112.00 104.85 7.15 1.40e+00 5.10e-01 2.61e+01 angle pdb=" C VAL C 320 " pdb=" N GLU C 321 " pdb=" CA GLU C 321 " ideal model delta sigma weight residual 121.54 130.20 -8.66 1.91e+00 2.74e-01 2.06e+01 angle pdb=" N PRO B 729 " pdb=" CD PRO B 729 " pdb=" CG PRO B 729 " ideal model delta sigma weight residual 103.20 97.17 6.03 1.50e+00 4.44e-01 1.61e+01 ... (remaining 48097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 21492 31.57 - 63.14: 424 63.14 - 94.71: 41 94.71 - 126.28: 3 126.28 - 157.85: 5 Dihedral angle restraints: 21965 sinusoidal: 9193 harmonic: 12772 Sorted by residual: dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 97.85 -157.85 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 92.11 -152.11 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 74.49 -134.49 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 21962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3968 0.043 - 0.085: 980 0.085 - 0.128: 421 0.128 - 0.170: 34 0.170 - 0.213: 2 Chirality restraints: 5405 Sorted by residual: chirality pdb=" CB ILE F 707 " pdb=" CA ILE F 707 " pdb=" CG1 ILE F 707 " pdb=" CG2 ILE F 707 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL C 407 " pdb=" CA VAL C 407 " pdb=" CG1 VAL C 407 " pdb=" CG2 VAL C 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.47e-01 chirality pdb=" CA GLU F 704 " pdb=" N GLU F 704 " pdb=" C GLU F 704 " pdb=" CB GLU F 704 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 5402 not shown) Planarity restraints: 6299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 245 " -0.082 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 246 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 728 " -0.065 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO B 729 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 729 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 729 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 371 " 0.056 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO B 372 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 372 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 372 " 0.045 5.00e-02 4.00e+02 ... (remaining 6296 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 268 2.56 - 3.15: 28494 3.15 - 3.73: 57360 3.73 - 4.32: 80036 4.32 - 4.90: 129918 Nonbonded interactions: 296076 Sorted by model distance: nonbonded pdb=" O1G ATP C 902 " pdb="MG MG C 904 " model vdw 1.978 2.170 nonbonded pdb=" OG1 THR C 252 " pdb="MG MG C 903 " model vdw 1.988 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 903 " model vdw 1.997 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 904 " model vdw 2.006 2.170 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 904 " model vdw 2.008 2.170 ... (remaining 296071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 5 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'B' and (resid 23 through 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 762)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.380 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 35576 Z= 0.173 Angle : 0.652 11.620 48102 Z= 0.355 Chirality : 0.044 0.213 5405 Planarity : 0.006 0.120 6299 Dihedral : 13.048 157.850 13675 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.04 (0.12), residues: 4391 helix: 1.09 (0.12), residues: 1914 sheet: 0.76 (0.20), residues: 624 loop : 0.42 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 711 TYR 0.019 0.002 TYR B 203 PHE 0.026 0.002 PHE F 771 TRP 0.011 0.001 TRP D 551 HIS 0.005 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (35576) covalent geometry : angle 0.65218 / 0.35 (48102) hydrogen bonds : bond 0.16722 / 11.41 ( 1617) hydrogen bonds : angle 6.47517 / 4.62 ( 4662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2745 time to fit residues: 116.2553 Evaluate side-chains 161 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS B 692 GLN C 36 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 533 ASN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 296 ASN F 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.100275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065820 restraints weight = 120059.741| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 4.72 r_work: 0.2935 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35576 Z= 0.168 Angle : 0.598 9.195 48102 Z= 0.303 Chirality : 0.044 0.191 5405 Planarity : 0.005 0.079 6299 Dihedral : 7.509 169.172 4888 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.57 % Favored : 98.34 % Rotamer: Outliers : 0.43 % Allowed : 4.72 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % 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: 1.22 (0.13), residues: 4391 helix: 1.30 (0.12), residues: 1971 sheet: 0.59 (0.20), residues: 644 loop : 0.51 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 711 TYR 0.020 0.002 TYR B 138 PHE 0.031 0.001 PHE B 163 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (35576) covalent geometry : angle 0.59819 / 0.30 (48102) hydrogen bonds : bond 0.04453 / 2.96 ( 1617) hydrogen bonds : angle 5.02203 / 3.61 ( 4662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.368 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 46 MET cc_start: 0.1020 (OUTLIER) cc_final: 0.0753 (ppp) REVERT: A 219 MET cc_start: 0.8225 (mmm) cc_final: 0.7980 (mmm) REVERT: A 449 MET cc_start: 0.8263 (tpt) cc_final: 0.7534 (tpt) REVERT: B 466 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8267 (mp0) REVERT: D 134 TYR cc_start: 0.5591 (m-80) cc_final: 0.4686 (m-80) REVERT: E 51 LEU cc_start: 0.7152 (mt) cc_final: 0.6915 (tp) REVERT: E 84 MET cc_start: 0.7557 (ttt) cc_final: 0.7095 (ttp) REVERT: F 219 MET cc_start: 0.9041 (mtt) cc_final: 0.8791 (mtm) outliers start: 16 outliers final: 2 residues processed: 185 average time/residue: 0.2341 time to fit residues: 70.1903 Evaluate side-chains 152 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 163 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 253 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 402 optimal weight: 6.9990 chunk 397 optimal weight: 7.9990 chunk 142 optimal weight: 0.0170 chunk 146 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 3.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN ** F 578 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 = 0.4085 r_free = 0.4085 target = 0.107427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069176 restraints weight = 99759.583| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.37 r_work: 0.2914 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 35576 Z= 0.224 Angle : 0.598 8.389 48102 Z= 0.302 Chirality : 0.045 0.173 5405 Planarity : 0.005 0.076 6299 Dihedral : 7.502 178.023 4888 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.98 % Favored : 97.95 % Rotamer: Outliers : 0.62 % Allowed : 6.99 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.21 (0.13), residues: 4391 helix: 1.38 (0.12), residues: 1970 sheet: 0.33 (0.19), residues: 676 loop : 0.52 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 323 TYR 0.015 0.002 TYR F 517 PHE 0.028 0.002 PHE E 163 TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (35576) covalent geometry : angle 0.59848 / 0.30 (48102) hydrogen bonds : bond 0.04243 / 2.82 ( 1617) hydrogen bonds : angle 4.81616 / 3.47 ( 4662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.124 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 219 MET cc_start: 0.8355 (mmm) cc_final: 0.7982 (mmm) REVERT: B 130 LEU cc_start: 0.5315 (mp) cc_final: 0.4900 (tt) REVERT: B 466 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8279 (mp0) REVERT: B 550 MET cc_start: 0.8889 (ptm) cc_final: 0.8366 (ttp) REVERT: E 46 MET cc_start: 0.2847 (mtp) cc_final: 0.2601 (mtp) REVERT: E 84 MET cc_start: 0.7806 (ttt) cc_final: 0.7438 (ttp) REVERT: E 427 MET cc_start: 0.9443 (mmm) cc_final: 0.9115 (mmm) REVERT: F 427 MET cc_start: 0.8971 (mpp) cc_final: 0.8665 (mpp) REVERT: F 442 MET cc_start: 0.8103 (mmm) cc_final: 0.7815 (mmm) REVERT: F 449 MET cc_start: 0.7264 (tpp) cc_final: 0.6977 (tpp) outliers start: 23 outliers final: 7 residues processed: 169 average time/residue: 0.2059 time to fit residues: 59.0551 Evaluate side-chains 152 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain E residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 325 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 380 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 337 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 103 GLN C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 384 HIS ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** F 603 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 = 0.4026 r_free = 0.4026 target = 0.095907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057954 restraints weight = 120541.364| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.44 r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 35576 Z= 0.397 Angle : 0.750 9.570 48102 Z= 0.377 Chirality : 0.050 0.208 5405 Planarity : 0.006 0.071 6299 Dihedral : 7.697 158.635 4888 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 1.21 % Allowed : 9.14 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4391 helix: 1.02 (0.11), residues: 1956 sheet: -0.16 (0.19), residues: 674 loop : 0.31 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG B 323 TYR 0.022 0.002 TYR C 755 PHE 0.022 0.002 PHE E 452 TRP 0.018 0.002 TRP A 476 HIS 0.008 0.002 HIS D 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.40 (35576) covalent geometry : angle 0.75034 / 0.38 (48102) hydrogen bonds : bond 0.04922 / 3.26 ( 1617) hydrogen bonds : angle 5.05213 / 3.63 ( 4662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.433 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 219 MET cc_start: 0.8519 (mmm) cc_final: 0.8034 (mmm) REVERT: A 442 MET cc_start: 0.7944 (tmm) cc_final: 0.7639 (mtm) REVERT: A 449 MET cc_start: 0.7598 (mmm) cc_final: 0.6764 (tpt) REVERT: B 466 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8377 (mp0) REVERT: D 46 MET cc_start: 0.5698 (mtm) cc_final: 0.5474 (mtm) REVERT: D 126 ILE cc_start: -0.0014 (OUTLIER) cc_final: -0.0344 (tp) REVERT: E 36 ASN cc_start: 0.5418 (OUTLIER) cc_final: 0.4008 (p0) REVERT: E 84 MET cc_start: 0.7637 (ttt) cc_final: 0.7288 (ttp) REVERT: E 163 PHE cc_start: 0.7254 (m-80) cc_final: 0.6401 (m-80) REVERT: E 173 TYR cc_start: 0.7080 (m-80) cc_final: 0.6687 (m-80) REVERT: E 332 MET cc_start: 0.8891 (mmm) cc_final: 0.8659 (mmm) REVERT: E 427 MET cc_start: 0.9383 (mmm) cc_final: 0.8915 (mmm) REVERT: F 427 MET cc_start: 0.9135 (mpp) cc_final: 0.8808 (mpp) REVERT: F 442 MET cc_start: 0.8082 (mmm) cc_final: 0.7821 (mmm) outliers start: 45 outliers final: 22 residues processed: 191 average time/residue: 0.2176 time to fit residues: 70.5537 Evaluate side-chains 172 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 134 TYR Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 6 optimal weight: 20.0000 chunk 330 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 440 optimal weight: 9.9990 chunk 253 optimal weight: 0.6980 chunk 302 optimal weight: 20.0000 chunk 339 optimal weight: 0.9980 chunk 248 optimal weight: 0.0980 chunk 109 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 538 ASN F 494 GLN ** F 578 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 = 0.4082 r_free = 0.4082 target = 0.102991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066211 restraints weight = 111007.337| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 4.07 r_work: 0.2944 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35576 Z= 0.113 Angle : 0.548 11.632 48102 Z= 0.274 Chirality : 0.043 0.161 5405 Planarity : 0.004 0.070 6299 Dihedral : 7.305 158.071 4888 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.59 % Favored : 98.34 % Rotamer: Outliers : 0.62 % Allowed : 10.08 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.18 (0.13), residues: 4391 helix: 1.45 (0.12), residues: 1956 sheet: 0.10 (0.20), residues: 661 loop : 0.47 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 638 TYR 0.011 0.001 TYR D 173 PHE 0.016 0.001 PHE B 163 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (35576) covalent geometry : angle 0.54757 / 0.27 (48102) hydrogen bonds : bond 0.03696 / 2.47 ( 1617) hydrogen bonds : angle 4.56764 / 3.29 ( 4662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.430 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 219 MET cc_start: 0.8574 (mmm) cc_final: 0.8057 (mmm) REVERT: A 442 MET cc_start: 0.8070 (tmm) cc_final: 0.7724 (mtm) REVERT: A 449 MET cc_start: 0.7619 (mmm) cc_final: 0.7140 (mmm) REVERT: B 173 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8086 (p90) REVERT: B 466 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8254 (mp0) REVERT: B 550 MET cc_start: 0.8897 (ptm) cc_final: 0.8478 (ttp) REVERT: E 84 MET cc_start: 0.7964 (ttt) cc_final: 0.7624 (ttp) REVERT: E 163 PHE cc_start: 0.7562 (m-80) cc_final: 0.6959 (m-10) REVERT: E 173 TYR cc_start: 0.7047 (m-80) cc_final: 0.6725 (m-80) REVERT: E 332 MET cc_start: 0.8907 (mmm) cc_final: 0.8576 (mmm) REVERT: E 427 MET cc_start: 0.9391 (mmm) cc_final: 0.9017 (mmm) REVERT: F 427 MET cc_start: 0.9114 (mpp) cc_final: 0.8821 (mpp) REVERT: F 442 MET cc_start: 0.8128 (mmm) cc_final: 0.7837 (mmm) outliers start: 23 outliers final: 6 residues processed: 171 average time/residue: 0.2160 time to fit residues: 62.7007 Evaluate side-chains 154 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 331 optimal weight: 7.9990 chunk 306 optimal weight: 50.0000 chunk 293 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 149 optimal weight: 0.4980 chunk 5 optimal weight: 50.0000 chunk 152 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 436 optimal weight: 1.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** F 578 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 = 0.4049 r_free = 0.4049 target = 0.097066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061397 restraints weight = 121868.117| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.14 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35576 Z= 0.218 Angle : 0.585 10.434 48102 Z= 0.290 Chirality : 0.044 0.202 5405 Planarity : 0.005 0.067 6299 Dihedral : 7.237 158.323 4888 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 0.88 % Allowed : 10.72 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.18 (0.13), residues: 4391 helix: 1.47 (0.12), residues: 1958 sheet: 0.05 (0.20), residues: 663 loop : 0.47 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 638 TYR 0.013 0.001 TYR F 517 PHE 0.015 0.001 PHE B 163 TRP 0.009 0.001 TRP A 476 HIS 0.012 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (35576) covalent geometry : angle 0.58532 / 0.29 (48102) hydrogen bonds : bond 0.03858 / 2.58 ( 1617) hydrogen bonds : angle 4.57661 / 3.30 ( 4662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.407 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 219 MET cc_start: 0.8607 (mmm) cc_final: 0.8075 (mmm) REVERT: A 442 MET cc_start: 0.8066 (tmm) cc_final: 0.7827 (mtm) REVERT: A 449 MET cc_start: 0.7669 (mmm) cc_final: 0.7198 (mmm) REVERT: B 173 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7876 (p90) REVERT: B 442 MET cc_start: 0.7545 (tpp) cc_final: 0.7289 (tmm) REVERT: B 466 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8301 (mp0) REVERT: B 550 MET cc_start: 0.8482 (ptm) cc_final: 0.7910 (ttp) REVERT: B 742 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8572 (t80) REVERT: D 19 GLN cc_start: 0.8496 (mp10) cc_final: 0.8155 (tm-30) REVERT: D 138 TYR cc_start: 0.6629 (t80) cc_final: 0.6238 (t80) REVERT: D 139 PHE cc_start: 0.7546 (m-10) cc_final: 0.7218 (m-10) REVERT: D 611 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8218 (mtp) REVERT: E 163 PHE cc_start: 0.7083 (m-80) cc_final: 0.6141 (m-80) REVERT: E 173 TYR cc_start: 0.7258 (m-80) cc_final: 0.6998 (m-80) REVERT: E 332 MET cc_start: 0.8927 (mmm) cc_final: 0.8531 (mmm) REVERT: E 427 MET cc_start: 0.9269 (mmm) cc_final: 0.8730 (mmm) REVERT: F 427 MET cc_start: 0.9183 (mpp) cc_final: 0.8909 (mpp) REVERT: F 442 MET cc_start: 0.8145 (mmm) cc_final: 0.7838 (mmm) outliers start: 33 outliers final: 19 residues processed: 173 average time/residue: 0.2117 time to fit residues: 62.3855 Evaluate side-chains 166 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 407 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 104 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 chunk 254 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 304 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN E 538 ASN ** F 578 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 = 0.4037 r_free = 0.4037 target = 0.096265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058716 restraints weight = 122593.523| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.48 r_work: 0.2905 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 35576 Z= 0.267 Angle : 0.619 10.422 48102 Z= 0.308 Chirality : 0.045 0.174 5405 Planarity : 0.005 0.065 6299 Dihedral : 7.235 160.472 4888 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 1.18 % Allowed : 10.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.05 (0.13), residues: 4391 helix: 1.38 (0.12), residues: 1957 sheet: -0.11 (0.19), residues: 691 loop : 0.43 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 638 TYR 0.014 0.002 TYR F 517 PHE 0.015 0.002 PHE B 163 TRP 0.010 0.001 TRP A 476 HIS 0.028 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (35576) covalent geometry : angle 0.61911 / 0.31 (48102) hydrogen bonds : bond 0.04036 / 2.70 ( 1617) hydrogen bonds : angle 4.64751 / 3.35 ( 4662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.450 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 219 MET cc_start: 0.8681 (mmm) cc_final: 0.8106 (mmm) REVERT: A 442 MET cc_start: 0.8176 (tmm) cc_final: 0.7905 (mtm) REVERT: A 449 MET cc_start: 0.7583 (mmm) cc_final: 0.6650 (tpt) REVERT: B 173 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8219 (p90) REVERT: B 466 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8370 (mp0) REVERT: B 550 MET cc_start: 0.9080 (ptm) cc_final: 0.8640 (ttp) REVERT: B 742 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8607 (t80) REVERT: D 19 GLN cc_start: 0.8449 (mp10) cc_final: 0.8147 (tm-30) REVERT: D 46 MET cc_start: 0.5408 (mtm) cc_final: 0.5166 (mtm) REVERT: D 126 ILE cc_start: 0.0011 (OUTLIER) cc_final: -0.0341 (tp) REVERT: D 611 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8482 (mtp) REVERT: E 84 MET cc_start: 0.7799 (ttt) cc_final: 0.7466 (ttp) REVERT: E 163 PHE cc_start: 0.7563 (m-80) cc_final: 0.6728 (m-80) REVERT: E 173 TYR cc_start: 0.7180 (m-80) cc_final: 0.6878 (m-80) REVERT: E 332 MET cc_start: 0.9039 (mmm) cc_final: 0.8589 (mmm) REVERT: E 427 MET cc_start: 0.9404 (mmm) cc_final: 0.8960 (mmm) REVERT: F 427 MET cc_start: 0.9112 (mpp) cc_final: 0.8838 (mpp) REVERT: F 442 MET cc_start: 0.8171 (mmm) cc_final: 0.7867 (mmm) outliers start: 44 outliers final: 29 residues processed: 180 average time/residue: 0.2168 time to fit residues: 66.3208 Evaluate side-chains 178 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 608 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 407 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 223 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 360 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 342 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 72 optimal weight: 0.0970 chunk 413 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 25 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 348 ASN E 538 ASN F 317 HIS ** F 578 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 = 0.4065 r_free = 0.4065 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.061309 restraints weight = 124975.374| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.44 r_work: 0.2969 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35576 Z= 0.102 Angle : 0.536 11.597 48102 Z= 0.264 Chirality : 0.042 0.191 5405 Planarity : 0.004 0.067 6299 Dihedral : 6.884 163.282 4888 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.87 % Favored : 98.06 % Rotamer: Outliers : 0.80 % Allowed : 11.52 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.26 (0.13), residues: 4391 helix: 1.53 (0.12), residues: 1992 sheet: 0.11 (0.20), residues: 666 loop : 0.49 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 25 TYR 0.012 0.001 TYR F 134 PHE 0.015 0.001 PHE B 163 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (35576) covalent geometry : angle 0.53574 / 0.26 (48102) hydrogen bonds : bond 0.03380 / 2.27 ( 1617) hydrogen bonds : angle 4.38403 / 3.17 ( 4662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.458 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 219 MET cc_start: 0.8609 (mmm) cc_final: 0.8061 (mmm) REVERT: A 388 MET cc_start: 0.7141 (ptp) cc_final: 0.6759 (tmm) REVERT: A 442 MET cc_start: 0.8197 (tmm) cc_final: 0.7889 (mtm) REVERT: A 449 MET cc_start: 0.7675 (mmm) cc_final: 0.7268 (mmm) REVERT: A 741 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7402 (tpt90) REVERT: B 173 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8055 (p90) REVERT: B 466 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8413 (mp0) REVERT: B 550 MET cc_start: 0.8957 (ptm) cc_final: 0.8636 (ttp) REVERT: B 742 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8424 (t80) REVERT: D 126 ILE cc_start: 0.0573 (OUTLIER) cc_final: 0.0180 (tp) REVERT: D 139 PHE cc_start: 0.7711 (m-10) cc_final: 0.7296 (m-10) REVERT: E 163 PHE cc_start: 0.7500 (m-80) cc_final: 0.6726 (m-80) REVERT: E 173 TYR cc_start: 0.7166 (m-80) cc_final: 0.6811 (m-80) REVERT: E 332 MET cc_start: 0.8951 (mmm) cc_final: 0.8547 (mmm) REVERT: E 427 MET cc_start: 0.9369 (mmm) cc_final: 0.8971 (mmm) REVERT: F 219 MET cc_start: 0.9027 (mtm) cc_final: 0.8785 (mpp) REVERT: F 275 MET cc_start: 0.9182 (mmm) cc_final: 0.8634 (mmp) REVERT: F 427 MET cc_start: 0.9047 (mpp) cc_final: 0.8794 (mpp) REVERT: F 442 MET cc_start: 0.8212 (mmm) cc_final: 0.7860 (mmm) outliers start: 30 outliers final: 14 residues processed: 174 average time/residue: 0.2106 time to fit residues: 61.5458 Evaluate side-chains 161 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 562 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 127 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 434 optimal weight: 9.9990 chunk 422 optimal weight: 20.0000 chunk 408 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 351 optimal weight: 0.3980 chunk 363 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 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 = 0.4047 r_free = 0.4047 target = 0.096897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059580 restraints weight = 121139.787| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.41 r_work: 0.2937 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.005 0.049 35576 Z= 0.205 Angle : 0.581 12.702 48102 Z= 0.286 Chirality : 0.044 0.175 5405 Planarity : 0.004 0.064 6299 Dihedral : 6.856 165.628 4888 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 0.67 % Allowed : 11.66 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.25 (0.13), residues: 4391 helix: 1.52 (0.12), residues: 1988 sheet: 0.09 (0.20), residues: 667 loop : 0.50 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 377 TYR 0.013 0.001 TYR E 138 PHE 0.014 0.001 PHE B 163 TRP 0.008 0.001 TRP A 476 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (35576) covalent geometry : angle 0.58056 / 0.29 (48102) hydrogen bonds : bond 0.03642 / 2.43 ( 1617) hydrogen bonds : angle 4.45219 / 3.22 ( 4662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.248 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 219 MET cc_start: 0.8666 (mmm) cc_final: 0.8100 (mmm) REVERT: A 317 HIS cc_start: 0.2385 (OUTLIER) cc_final: 0.0833 (p-80) REVERT: A 388 MET cc_start: 0.7200 (ptp) cc_final: 0.6831 (tmm) REVERT: A 442 MET cc_start: 0.8160 (tmm) cc_final: 0.7906 (mtm) REVERT: A 449 MET cc_start: 0.7808 (mmm) cc_final: 0.7383 (mmm) REVERT: A 741 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7351 (tpt90) REVERT: B 173 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8201 (p90) REVERT: B 388 MET cc_start: 0.8573 (ptp) cc_final: 0.8166 (pmm) REVERT: B 449 MET cc_start: 0.5910 (mmm) cc_final: 0.5500 (tpp) REVERT: B 466 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8424 (mp0) REVERT: B 550 MET cc_start: 0.9038 (ptm) cc_final: 0.8657 (ttp) REVERT: B 742 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8482 (t80) REVERT: D 19 GLN cc_start: 0.8439 (mp10) cc_final: 0.8146 (tm-30) REVERT: D 126 ILE cc_start: -0.0257 (OUTLIER) cc_final: -0.0660 (tp) REVERT: D 139 PHE cc_start: 0.7689 (m-10) cc_final: 0.7439 (m-10) REVERT: E 163 PHE cc_start: 0.7525 (m-80) cc_final: 0.6657 (m-80) REVERT: E 173 TYR cc_start: 0.7199 (m-80) cc_final: 0.6839 (m-80) REVERT: E 332 MET cc_start: 0.9000 (mmm) cc_final: 0.8583 (mmm) REVERT: E 427 MET cc_start: 0.9368 (mmm) cc_final: 0.8934 (mmm) REVERT: E 740 MET cc_start: 0.9141 (mmm) cc_final: 0.8897 (mmm) REVERT: F 427 MET cc_start: 0.9082 (mpp) cc_final: 0.8806 (mpp) REVERT: F 442 MET cc_start: 0.8227 (mmm) cc_final: 0.7889 (mmm) outliers start: 25 outliers final: 19 residues processed: 165 average time/residue: 0.2159 time to fit residues: 60.4811 Evaluate side-chains 166 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 415 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 424 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 263 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 392 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.097837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.060690 restraints weight = 123424.351| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.46 r_work: 0.2958 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35576 Z= 0.122 Angle : 0.551 13.386 48102 Z= 0.270 Chirality : 0.043 0.176 5405 Planarity : 0.004 0.064 6299 Dihedral : 6.740 165.819 4888 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 0.64 % Allowed : 11.84 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.27 (0.13), residues: 4391 helix: 1.54 (0.12), residues: 2002 sheet: 0.10 (0.20), residues: 667 loop : 0.49 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.012 0.001 TYR F 134 PHE 0.014 0.001 PHE B 163 TRP 0.007 0.001 TRP A 476 HIS 0.015 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (35576) covalent geometry : angle 0.55104 / 0.27 (48102) hydrogen bonds : bond 0.03395 / 2.27 ( 1617) hydrogen bonds : angle 4.35549 / 3.15 ( 4662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.939 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 219 MET cc_start: 0.8627 (mmm) cc_final: 0.8044 (mmm) REVERT: A 388 MET cc_start: 0.7153 (ptp) cc_final: 0.6769 (tmm) REVERT: A 442 MET cc_start: 0.8229 (tmm) cc_final: 0.7965 (mtm) REVERT: A 449 MET cc_start: 0.7695 (mmm) cc_final: 0.7282 (mmm) REVERT: A 741 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7336 (tpt90) REVERT: B 173 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8239 (p90) REVERT: B 449 MET cc_start: 0.5996 (mmm) cc_final: 0.5567 (tpp) REVERT: B 466 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8394 (mp0) REVERT: B 550 MET cc_start: 0.9040 (ptm) cc_final: 0.8708 (ttp) REVERT: B 742 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8476 (t80) REVERT: D 126 ILE cc_start: 0.0369 (OUTLIER) cc_final: -0.0061 (tp) REVERT: D 139 PHE cc_start: 0.7695 (m-10) cc_final: 0.7425 (m-10) REVERT: E 163 PHE cc_start: 0.7498 (m-80) cc_final: 0.6656 (m-80) REVERT: E 173 TYR cc_start: 0.7068 (m-80) cc_final: 0.6728 (m-80) REVERT: E 332 MET cc_start: 0.8997 (mmm) cc_final: 0.8583 (mmm) REVERT: E 427 MET cc_start: 0.9367 (mmm) cc_final: 0.8963 (mmm) REVERT: E 740 MET cc_start: 0.9129 (mmm) cc_final: 0.8907 (mmm) REVERT: F 219 MET cc_start: 0.9064 (mtm) cc_final: 0.8834 (mpp) REVERT: F 427 MET cc_start: 0.9049 (mpp) cc_final: 0.8778 (mpp) REVERT: F 442 MET cc_start: 0.8212 (mmm) cc_final: 0.7830 (mmm) outliers start: 24 outliers final: 18 residues processed: 162 average time/residue: 0.1969 time to fit residues: 54.0458 Evaluate side-chains 163 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 741 ARG Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 362 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 99 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 28 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 160 optimal weight: 0.1980 chunk 400 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 332 optimal weight: 0.6980 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.097307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060237 restraints weight = 121533.809| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.42 r_work: 0.2946 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35576 Z= 0.150 Angle : 0.553 13.953 48102 Z= 0.271 Chirality : 0.043 0.174 5405 Planarity : 0.004 0.064 6299 Dihedral : 6.687 167.883 4888 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 0.70 % Allowed : 11.74 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.31 (0.13), residues: 4391 helix: 1.59 (0.12), residues: 1987 sheet: 0.09 (0.20), residues: 667 loop : 0.51 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 377 TYR 0.014 0.001 TYR E 138 PHE 0.014 0.001 PHE B 163 TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (35576) covalent geometry : angle 0.55316 / 0.27 (48102) hydrogen bonds : bond 0.03425 / 2.29 ( 1617) hydrogen bonds : angle 4.34647 / 3.14 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11418.88 seconds wall clock time: 195 minutes 19.89 seconds (11719.89 seconds total)