Starting phenix.real_space_refine on Fri Mar 6 22:22:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lmz_23443/03_2026/7lmz_23443.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmz_23443/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lmz_23443/03_2026/7lmz_23443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmz_23443/03_2026/7lmz_23443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lmz_23443/03_2026/7lmz_23443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmz_23443/03_2026/7lmz_23443.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.97, per 1000 atoms: 0.23 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 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: 1.32 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: 7.22 Time building geometry restraints manager: 3.68 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: 21597 31.57 - 63.14: 543 63.14 - 94.71: 65 94.71 - 126.28: 3 126.28 - 157.85: 5 Dihedral angle restraints: 22213 sinusoidal: 9441 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 22210 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.500 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 14.061 157.850 13923 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 covalent geometry : bond 0.00396 (35576) covalent geometry : angle 0.65218 (48102) hydrogen bonds : bond 0.16722 ( 1617) hydrogen bonds : angle 6.47517 ( 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 : 1.349 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: 0.2770 time to fit residues: 117.1449 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 : 1.384 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 F 602 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.100493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065535 restraints weight = 119715.636| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.62 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35576 Z= 0.170 Angle : 0.602 9.706 48102 Z= 0.306 Chirality : 0.044 0.186 5405 Planarity : 0.005 0.078 6299 Dihedral : 11.140 167.710 5136 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer: Outliers : 0.35 % Allowed : 4.72 % Favored : 94.94 % 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: 1.32 (0.12), residues: 1957 sheet: 0.59 (0.20), residues: 645 loop : 0.50 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 711 TYR 0.022 0.001 TYR B 138 PHE 0.025 0.001 PHE B 163 TRP 0.011 0.001 TRP A 476 HIS 0.006 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00393 (35576) covalent geometry : angle 0.60152 (48102) hydrogen bonds : bond 0.04680 ( 1617) hydrogen bonds : angle 5.12322 ( 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 183 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.344 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 449 MET cc_start: 0.8146 (tpt) cc_final: 0.7490 (tpt) REVERT: B 466 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8127 (mp0) REVERT: D 134 TYR cc_start: 0.5630 (m-80) cc_final: 0.4650 (m-80) REVERT: E 84 MET cc_start: 0.7367 (ttt) cc_final: 0.6741 (ttp) REVERT: E 163 PHE cc_start: 0.6812 (m-80) cc_final: 0.6607 (m-80) REVERT: F 173 TYR cc_start: 0.3245 (p90) cc_final: 0.3009 (p90) REVERT: F 219 MET cc_start: 0.9020 (mtt) cc_final: 0.8739 (mtm) REVERT: F 442 MET cc_start: 0.8091 (mmm) cc_final: 0.7796 (mmm) REVERT: F 449 MET cc_start: 0.7512 (tpp) cc_final: 0.6990 (tpp) outliers start: 13 outliers final: 3 residues processed: 177 average time/residue: 0.2265 time to fit residues: 65.5108 Evaluate side-chains 153 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain C residue 344 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 253 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 39 optimal weight: 20.0000 chunk 402 optimal weight: 10.0000 chunk 397 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN F 578 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.099999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.065669 restraints weight = 120227.094| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.35 r_work: 0.2957 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35576 Z= 0.143 Angle : 0.556 8.515 48102 Z= 0.281 Chirality : 0.044 0.179 5405 Planarity : 0.005 0.078 6299 Dihedral : 10.868 171.511 5136 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Rotamer: Outliers : 0.59 % Allowed : 6.62 % Favored : 92.79 % 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: 1.44 (0.12), residues: 1983 sheet: 0.39 (0.20), residues: 655 loop : 0.50 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 323 TYR 0.014 0.001 TYR F 517 PHE 0.019 0.001 PHE B 163 TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00327 (35576) covalent geometry : angle 0.55633 (48102) hydrogen bonds : bond 0.03924 ( 1617) hydrogen bonds : angle 4.76533 ( 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 180 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7077 (pp30) cc_final: 0.6845 (mm-40) REVERT: A 219 MET cc_start: 0.8208 (mmm) cc_final: 0.7979 (mmm) REVERT: A 449 MET cc_start: 0.8191 (tpt) cc_final: 0.7827 (mmm) REVERT: B 466 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8245 (mp0) REVERT: B 550 MET cc_start: 0.8918 (ptm) cc_final: 0.8527 (ttp) REVERT: B 740 MET cc_start: 0.8799 (tpt) cc_final: 0.8470 (tpt) REVERT: E 51 LEU cc_start: 0.6706 (tp) cc_final: 0.6457 (tt) REVERT: E 84 MET cc_start: 0.7685 (ttt) cc_final: 0.7303 (ttp) REVERT: E 332 MET cc_start: 0.8969 (mmm) cc_final: 0.8468 (mmm) REVERT: F 344 MET cc_start: 0.8543 (mtm) cc_final: 0.8061 (mtm) REVERT: F 427 MET cc_start: 0.8898 (mpp) cc_final: 0.8644 (mpp) REVERT: F 442 MET cc_start: 0.8232 (mmm) cc_final: 0.7902 (mmm) REVERT: F 449 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7140 (tpp) outliers start: 22 outliers final: 5 residues processed: 173 average time/residue: 0.2107 time to fit residues: 60.2295 Evaluate side-chains 155 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain F residue 449 MET Chi-restraints excluded: chain F residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 325 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 423 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 357 optimal weight: 4.9990 chunk 380 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN C 36 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.106803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067796 restraints weight = 98264.557| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.44 r_work: 0.2883 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 35576 Z= 0.313 Angle : 0.668 9.370 48102 Z= 0.335 Chirality : 0.047 0.188 5405 Planarity : 0.005 0.073 6299 Dihedral : 11.039 173.355 5136 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.40 % Rotamer: Outliers : 0.86 % Allowed : 8.23 % Favored : 90.92 % 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: 1.06 (0.13), residues: 4391 helix: 1.31 (0.12), residues: 1955 sheet: 0.12 (0.19), residues: 662 loop : 0.44 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 635 TYR 0.019 0.002 TYR C 173 PHE 0.017 0.002 PHE E 452 TRP 0.014 0.001 TRP A 476 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00727 (35576) covalent geometry : angle 0.66780 (48102) hydrogen bonds : bond 0.04432 ( 1617) hydrogen bonds : angle 4.84031 ( 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 185 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.046 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: 0.8285 (mmm) cc_final: 0.7968 (mmm) REVERT: A 442 MET cc_start: 0.7960 (tmm) cc_final: 0.7521 (mtm) REVERT: A 449 MET cc_start: 0.7805 (tpt) cc_final: 0.7123 (tpt) REVERT: B 130 LEU cc_start: 0.5297 (mp) cc_final: 0.4881 (tt) REVERT: B 219 MET cc_start: 0.8104 (mmt) cc_final: 0.7585 (mmt) REVERT: B 466 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8405 (mp0) REVERT: D 126 ILE cc_start: 0.1026 (OUTLIER) cc_final: 0.0405 (tp) REVERT: D 508 MET cc_start: 0.9031 (mmm) cc_final: 0.8762 (mmm) REVERT: E 173 TYR cc_start: 0.6912 (m-80) cc_final: 0.6516 (m-80) REVERT: F 344 MET cc_start: 0.8691 (mtm) cc_final: 0.8412 (mtm) REVERT: F 427 MET cc_start: 0.9035 (mpp) cc_final: 0.8741 (mpp) REVERT: F 442 MET cc_start: 0.8207 (mmm) cc_final: 0.7892 (mmm) outliers start: 32 outliers final: 12 residues processed: 174 average time/residue: 0.2087 time to fit residues: 60.0148 Evaluate side-chains 161 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 492 LEU 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 126 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain F residue 134 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 6 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 440 optimal weight: 0.0770 chunk 253 optimal weight: 0.8980 chunk 302 optimal weight: 30.0000 chunk 339 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 348 ASN F 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.099992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064914 restraints weight = 119188.697| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.29 r_work: 0.2940 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35576 Z= 0.110 Angle : 0.534 12.410 48102 Z= 0.267 Chirality : 0.043 0.169 5405 Planarity : 0.004 0.072 6299 Dihedral : 10.528 171.127 5136 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.59 % Favored : 98.36 % Rotamer: Outliers : 0.64 % Allowed : 9.22 % Favored : 90.14 % 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: 1.34 (0.13), residues: 4391 helix: 1.59 (0.12), residues: 1953 sheet: 0.29 (0.20), residues: 661 loop : 0.49 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 323 TYR 0.010 0.001 TYR D 517 PHE 0.015 0.001 PHE B 163 TRP 0.006 0.001 TRP A 476 HIS 0.003 0.000 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00243 (35576) covalent geometry : angle 0.53357 (48102) hydrogen bonds : bond 0.03529 ( 1617) hydrogen bonds : angle 4.49483 ( 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 179 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.315 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 50 GLN cc_start: 0.7172 (pp30) cc_final: 0.6948 (mm-40) REVERT: A 219 MET cc_start: 0.8442 (mmm) cc_final: 0.8025 (mmm) REVERT: A 442 MET cc_start: 0.7989 (tmm) cc_final: 0.7553 (mtm) REVERT: A 449 MET cc_start: 0.7821 (tpt) cc_final: 0.7156 (tpt) REVERT: B 466 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8291 (mp0) REVERT: D 139 PHE cc_start: 0.7549 (m-10) cc_final: 0.7053 (m-10) REVERT: D 608 MET cc_start: 0.9358 (mtp) cc_final: 0.9155 (mtm) REVERT: E 84 MET cc_start: 0.7804 (ttt) cc_final: 0.7448 (ttp) REVERT: E 163 PHE cc_start: 0.7475 (m-80) cc_final: 0.6882 (m-10) REVERT: E 173 TYR cc_start: 0.6843 (m-80) cc_final: 0.6508 (m-80) REVERT: E 332 MET cc_start: 0.8915 (mmm) cc_final: 0.8539 (mmm) REVERT: F 344 MET cc_start: 0.8701 (mtm) cc_final: 0.8446 (mtm) REVERT: F 427 MET cc_start: 0.9080 (mpp) cc_final: 0.8839 (mpp) REVERT: F 442 MET cc_start: 0.8216 (mmm) cc_final: 0.7924 (mmm) outliers start: 24 outliers final: 9 residues processed: 174 average time/residue: 0.2046 time to fit residues: 60.1265 Evaluate side-chains 157 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain D residue 235 VAL 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: 0.4980 chunk 293 optimal weight: 7.9990 chunk 360 optimal weight: 0.9990 chunk 233 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 168 optimal weight: 0.1980 chunk 436 optimal weight: 6.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN ** C 533 ASN ** 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 = 0.4103 r_free = 0.4103 target = 0.107064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071684 restraints weight = 103958.324| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 4.87 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2396 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= 0.102 Angle : 0.522 11.641 48102 Z= 0.257 Chirality : 0.042 0.250 5405 Planarity : 0.004 0.073 6299 Dihedral : 10.273 166.697 5136 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.73 % Favored : 98.20 % Rotamer: Outliers : 0.64 % Allowed : 9.81 % Favored : 89.55 % 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: 1.40 (0.13), residues: 4391 helix: 1.65 (0.12), residues: 1972 sheet: 0.30 (0.20), residues: 661 loop : 0.50 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 693 TYR 0.010 0.001 TYR D 173 PHE 0.014 0.001 PHE B 163 TRP 0.006 0.001 TRP A 476 HIS 0.002 0.000 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00222 (35576) covalent geometry : angle 0.52151 (48102) hydrogen bonds : bond 0.03296 ( 1617) hydrogen bonds : angle 4.36588 ( 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 177 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8532 (mmm) cc_final: 0.8086 (mmm) REVERT: A 442 MET cc_start: 0.7921 (tmm) cc_final: 0.7557 (mtm) REVERT: A 449 MET cc_start: 0.7987 (tpt) cc_final: 0.7178 (tpt) REVERT: B 130 LEU cc_start: 0.6119 (mp) cc_final: 0.5710 (tt) REVERT: B 388 MET cc_start: 0.8498 (ptp) cc_final: 0.8294 (pmm) REVERT: B 466 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8016 (mp0) REVERT: B 742 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8531 (t80) REVERT: C 192 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8552 (mm-30) REVERT: D 139 PHE cc_start: 0.7362 (m-10) cc_final: 0.6957 (m-10) REVERT: E 84 MET cc_start: 0.7404 (ttt) cc_final: 0.6937 (ttp) REVERT: E 163 PHE cc_start: 0.6988 (m-80) cc_final: 0.6058 (m-10) REVERT: F 158 MET cc_start: 0.4977 (pmm) cc_final: 0.4589 (pmm) REVERT: F 427 MET cc_start: 0.9106 (mpp) cc_final: 0.8833 (mpp) REVERT: F 442 MET cc_start: 0.8203 (mmm) cc_final: 0.7884 (mmm) REVERT: F 449 MET cc_start: 0.6804 (tpp) cc_final: 0.6545 (tpp) outliers start: 24 outliers final: 13 residues processed: 173 average time/residue: 0.2015 time to fit residues: 59.7391 Evaluate side-chains 159 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 761 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 104 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 226 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN D 384 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.107045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069542 restraints weight = 99537.761| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.63 r_work: 0.2904 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35576 Z= 0.212 Angle : 0.588 10.734 48102 Z= 0.291 Chirality : 0.044 0.241 5405 Planarity : 0.005 0.067 6299 Dihedral : 10.451 162.322 5136 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Rotamer: Outliers : 0.86 % Allowed : 10.05 % Favored : 89.09 % 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: 1.33 (0.13), residues: 4391 helix: 1.60 (0.12), residues: 1968 sheet: 0.16 (0.19), residues: 674 loop : 0.53 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 89 TYR 0.014 0.001 TYR F 517 PHE 0.014 0.001 PHE B 163 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00492 (35576) covalent geometry : angle 0.58818 (48102) hydrogen bonds : bond 0.03729 ( 1617) hydrogen bonds : angle 4.46368 ( 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 181 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.271 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: 0.8586 (mmm) cc_final: 0.8137 (mmm) REVERT: A 442 MET cc_start: 0.8056 (tmm) cc_final: 0.7733 (mtm) REVERT: A 449 MET cc_start: 0.7746 (tpt) cc_final: 0.7134 (tpt) REVERT: B 130 LEU cc_start: 0.5324 (mp) cc_final: 0.4958 (tt) REVERT: B 466 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8381 (mp0) REVERT: B 742 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8635 (t80) REVERT: C 192 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: D 126 ILE cc_start: 0.0976 (OUTLIER) cc_final: 0.0316 (tp) REVERT: D 139 PHE cc_start: 0.7531 (m-10) cc_final: 0.7143 (m-10) REVERT: E 84 MET cc_start: 0.7890 (ttt) cc_final: 0.7590 (ttp) REVERT: E 163 PHE cc_start: 0.7524 (m-80) cc_final: 0.6803 (m-80) REVERT: E 173 TYR cc_start: 0.6594 (m-80) cc_final: 0.6336 (m-10) REVERT: F 427 MET cc_start: 0.9088 (mpp) cc_final: 0.8820 (mpp) REVERT: F 442 MET cc_start: 0.8203 (mmm) cc_final: 0.7887 (mmm) REVERT: F 449 MET cc_start: 0.7211 (tpp) cc_final: 0.6895 (tpp) outliers start: 32 outliers final: 17 residues processed: 172 average time/residue: 0.2001 time to fit residues: 58.4666 Evaluate side-chains 168 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 611 MET 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 B residue 742 PHE Chi-restraints excluded: chain B residue 761 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 752 ILE Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 762 LEU 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: 0.5980 chunk 360 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 413 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.107278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.071334 restraints weight = 100405.917| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 5.06 r_work: 0.2909 rms_B_bonded: 5.04 restraints_weight: 2.0000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35576 Z= 0.129 Angle : 0.549 11.969 48102 Z= 0.269 Chirality : 0.043 0.210 5405 Planarity : 0.004 0.066 6299 Dihedral : 10.227 163.619 5136 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.95 % Rotamer: Outliers : 0.67 % Allowed : 10.37 % Favored : 88.96 % 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: 1.42 (0.13), residues: 4391 helix: 1.66 (0.12), residues: 1967 sheet: 0.25 (0.20), residues: 662 loop : 0.56 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 159 TYR 0.011 0.001 TYR D 173 PHE 0.014 0.001 PHE B 163 TRP 0.007 0.001 TRP A 476 HIS 0.003 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00298 (35576) covalent geometry : angle 0.54889 (48102) hydrogen bonds : bond 0.03393 ( 1617) hydrogen bonds : angle 4.34690 ( 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 174 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.335 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: A 219 MET cc_start: 0.8587 (mmm) cc_final: 0.8126 (mmm) REVERT: A 442 MET cc_start: 0.8099 (tmm) cc_final: 0.7755 (mtm) REVERT: A 449 MET cc_start: 0.7640 (tpt) cc_final: 0.6946 (tpt) REVERT: B 130 LEU cc_start: 0.5274 (mp) cc_final: 0.4888 (tt) REVERT: B 173 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.8081 (p90) REVERT: B 449 MET cc_start: 0.6070 (mmm) cc_final: 0.5745 (mmt) REVERT: B 466 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8408 (mp0) REVERT: B 742 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8568 (t80) REVERT: C 192 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: D 126 ILE cc_start: 0.0262 (OUTLIER) cc_final: -0.0101 (tp) REVERT: D 139 PHE cc_start: 0.7567 (m-10) cc_final: 0.7216 (m-10) REVERT: E 84 MET cc_start: 0.7842 (ttt) cc_final: 0.7493 (ttp) REVERT: E 163 PHE cc_start: 0.7606 (m-80) cc_final: 0.6867 (m-80) REVERT: F 84 MET cc_start: 0.4145 (tmm) cc_final: 0.3859 (tmm) REVERT: F 427 MET cc_start: 0.9087 (mpp) cc_final: 0.8796 (mpp) REVERT: F 442 MET cc_start: 0.8259 (mmm) cc_final: 0.7906 (mmm) REVERT: F 449 MET cc_start: 0.7419 (tpp) cc_final: 0.7065 (tpp) outliers start: 25 outliers final: 19 residues processed: 169 average time/residue: 0.1964 time to fit residues: 57.4828 Evaluate side-chains 169 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 286 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 59 LEU 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 445 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 761 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 127 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 434 optimal weight: 9.9990 chunk 422 optimal weight: 20.0000 chunk 408 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 351 optimal weight: 0.9980 chunk 363 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.108273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072839 restraints weight = 94847.321| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.98 r_work: 0.2913 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35576 Z= 0.232 Angle : 0.603 12.937 48102 Z= 0.298 Chirality : 0.045 0.183 5405 Planarity : 0.005 0.062 6299 Dihedral : 10.399 166.276 5136 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 0.86 % Allowed : 10.56 % Favored : 88.59 % 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: 1.24 (0.13), residues: 4391 helix: 1.48 (0.12), residues: 1982 sheet: 0.11 (0.19), residues: 687 loop : 0.54 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 155 TYR 0.014 0.001 TYR C 755 PHE 0.014 0.002 PHE B 163 TRP 0.009 0.001 TRP A 476 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00539 (35576) covalent geometry : angle 0.60275 (48102) hydrogen bonds : bond 0.03779 ( 1617) hydrogen bonds : angle 4.47503 ( 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 178 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8602 (mmm) cc_final: 0.8118 (mmm) REVERT: A 442 MET cc_start: 0.8097 (tmm) cc_final: 0.7785 (mtm) REVERT: A 449 MET cc_start: 0.7562 (tpt) cc_final: 0.6973 (tpt) REVERT: B 130 LEU cc_start: 0.5733 (mp) cc_final: 0.5351 (tt) REVERT: B 173 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7994 (p90) REVERT: B 449 MET cc_start: 0.6092 (mmm) cc_final: 0.5790 (tpp) REVERT: B 466 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8416 (mp0) REVERT: B 742 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8660 (t80) REVERT: C 192 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: D 126 ILE cc_start: 0.0260 (OUTLIER) cc_final: -0.0188 (tp) REVERT: D 139 PHE cc_start: 0.7544 (m-10) cc_final: 0.7212 (m-10) REVERT: E 84 MET cc_start: 0.7798 (ttt) cc_final: 0.7435 (ttp) REVERT: E 163 PHE cc_start: 0.7543 (m-80) cc_final: 0.6709 (m-80) REVERT: E 173 TYR cc_start: 0.6740 (m-80) cc_final: 0.6464 (m-10) REVERT: F 275 MET cc_start: 0.9321 (mmp) cc_final: 0.8920 (mmp) REVERT: F 427 MET cc_start: 0.9085 (mpp) cc_final: 0.8827 (mpp) REVERT: F 442 MET cc_start: 0.8255 (mmm) cc_final: 0.7906 (mmm) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.1983 time to fit residues: 57.8384 Evaluate side-chains 170 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 611 MET 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 445 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 192 GLU 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 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 608 MET 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: 7.9990 chunk 356 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 424 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 156 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN F 317 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.107675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071464 restraints weight = 99152.843| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 5.07 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2827 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= 0.122 Angle : 0.556 13.919 48102 Z= 0.273 Chirality : 0.043 0.188 5405 Planarity : 0.004 0.063 6299 Dihedral : 10.097 167.768 5136 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.84 % Favored : 98.09 % Rotamer: Outliers : 0.80 % Allowed : 10.85 % Favored : 88.34 % 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: 1.36 (0.13), residues: 4391 helix: 1.58 (0.12), residues: 1990 sheet: 0.25 (0.20), residues: 665 loop : 0.54 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 155 TYR 0.011 0.001 TYR F 517 PHE 0.014 0.001 PHE B 163 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00279 (35576) covalent geometry : angle 0.55619 (48102) hydrogen bonds : bond 0.03392 ( 1617) hydrogen bonds : angle 4.34260 ( 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 177 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8579 (mmm) cc_final: 0.8079 (mmm) REVERT: A 442 MET cc_start: 0.8048 (tmm) cc_final: 0.7797 (mtm) REVERT: A 449 MET cc_start: 0.7504 (tpt) cc_final: 0.6913 (tpt) REVERT: B 130 LEU cc_start: 0.5776 (mp) cc_final: 0.5484 (tt) REVERT: B 173 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7782 (p90) REVERT: B 267 PHE cc_start: 0.7565 (t80) cc_final: 0.7354 (t80) REVERT: B 449 MET cc_start: 0.6057 (mmm) cc_final: 0.5698 (tpp) REVERT: B 466 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8354 (mp0) REVERT: B 742 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8557 (t80) REVERT: C 192 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: D 117 LEU cc_start: 0.7331 (mt) cc_final: 0.7120 (tp) REVERT: D 126 ILE cc_start: 0.0324 (OUTLIER) cc_final: -0.0050 (tp) REVERT: D 139 PHE cc_start: 0.7342 (m-10) cc_final: 0.6952 (m-10) REVERT: E 84 MET cc_start: 0.7457 (ttt) cc_final: 0.6991 (ttp) REVERT: E 163 PHE cc_start: 0.7270 (m-80) cc_final: 0.6320 (m-80) REVERT: F 84 MET cc_start: 0.3628 (tmm) cc_final: 0.2774 (tmm) REVERT: F 219 MET cc_start: 0.9039 (ptp) cc_final: 0.8774 (ptp) REVERT: F 427 MET cc_start: 0.9072 (mpp) cc_final: 0.8849 (mpp) REVERT: F 442 MET cc_start: 0.8254 (mmm) cc_final: 0.7936 (mmm) outliers start: 30 outliers final: 25 residues processed: 171 average time/residue: 0.1953 time to fit residues: 57.2230 Evaluate side-chains 172 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 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 286 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 316 THR 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 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 445 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 192 GLU 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 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 608 MET 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: 3.9990 chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 305 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 400 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.098870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063536 restraints weight = 118115.494| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.18 r_work: 0.2906 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35576 Z= 0.169 Angle : 0.579 13.882 48102 Z= 0.284 Chirality : 0.043 0.168 5405 Planarity : 0.004 0.063 6299 Dihedral : 10.082 169.755 5136 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.88 % Allowed : 10.69 % Favored : 88.42 % 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: 1.32 (0.13), residues: 4391 helix: 1.55 (0.12), residues: 1996 sheet: 0.20 (0.20), residues: 666 loop : 0.52 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 65 TYR 0.016 0.001 TYR E 173 PHE 0.014 0.001 PHE B 163 TRP 0.008 0.001 TRP A 476 HIS 0.020 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00392 (35576) covalent geometry : angle 0.57869 (48102) hydrogen bonds : bond 0.03491 ( 1617) hydrogen bonds : angle 4.36375 ( 4662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10970.27 seconds wall clock time: 187 minutes 18.93 seconds (11238.93 seconds total)