Starting phenix.real_space_refine on Fri Mar 6 22:18:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.map" model { file = "/net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln0_23444/03_2026/7ln0_23444.cif" } resolution = 2.98 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= 0.003 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 7 5.21 5 S 178 5.16 5 C 21902 2.51 5 N 6208 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 91 residue(s): 0.04s 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: 34983 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: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5793 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 36 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: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 7.96, per 1000 atoms: 0.23 Number of scatterers: 34983 At special positions: 0 Unit cell: (164.765, 171.143, 132.875, 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 7 11.99 O 6656 8.00 N 6208 7.00 C 21902 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 1.6 seconds 8782 Ramachandran restraints generated. 4391 Oldfield, 0 Emsley, 4391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8290 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 28 sheets defined 51.5% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.713A 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 removed outlier: 3.527A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.797A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.657A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.584A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.620A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.832A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.631A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.038A 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 removed outlier: 3.540A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.569A 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: 3.796A pdb=" N ILE A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 714 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.854A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.716A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.950A pdb=" N GLU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.551A 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: 4.393A 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: 3.940A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 removed outlier: 3.808A pdb=" N ALA B 255 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.689A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.761A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.509A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.540A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.752A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) 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: 3.713A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 removed outlier: 3.519A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 578 through 583 removed outlier: 4.290A pdb=" N ILE B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.750A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.568A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 Processing helix chain 'C' and resid 43 through 49 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 92 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.699A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 removed outlier: 3.541A 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: 4.382A 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: 4.224A 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 271 through 275 removed outlier: 4.048A pdb=" N MET C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.729A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.504A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 428 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 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: 3.633A 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 547 No H-bonds generated for 'chain 'C' and resid 545 through 547' Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 578 through 583 removed outlier: 4.276A pdb=" N ILE C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.793A 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 741 Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.739A pdb=" N GLY C 767 " --> pdb=" O GLN C 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.875A pdb=" N LYS D 18 " --> pdb=" O ALA D 15 " (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: 3.539A 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 139 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.525A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) 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: 4.403A 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 271 through 275 removed outlier: 4.167A pdb=" N MET D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 271 through 275' Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.207A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.519A 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: 3.804A 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 547 removed outlier: 3.846A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 569 Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.849A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 4.319A pdb=" N GLY D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.921A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (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 741 Processing helix chain 'D' and resid 748 through 767 removed outlier: 4.035A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.790A 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 removed outlier: 3.789A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 4.069A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 272 through 275 Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.573A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.250A 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 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.562A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.602A 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: 4.367A pdb=" N GLU E 466 " --> pdb=" O ALA E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 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: 4.123A 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 543 through 547 removed outlier: 4.093A pdb=" N LEU E 547 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 569 Processing helix chain 'E' and resid 578 through 583 removed outlier: 3.934A pdb=" N ILE E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 611 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.619A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.664A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 120 through 123 Processing helix chain 'F' and resid 129 through 134 removed outlier: 3.717A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.984A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.614A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.304A 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 removed outlier: 3.582A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.925A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.628A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.690A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 426 Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.808A 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: 3.505A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (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: 3.940A 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: 3.820A pdb=" N LEU F 634 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 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 Processing helix chain 'F' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 29 removed outlier: 7.827A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.922A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA A 177 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ARG A 113 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N ASP A 179 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N HIS A 115 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N VAL A 181 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N LEU A 117 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N HIS A 183 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.860A 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: 6.153A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.563A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 100 removed outlier: 5.908A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.972A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.660A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.520A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.511A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 29 removed outlier: 7.749A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 154 removed outlier: 3.562A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.883A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.384A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 543 removed outlier: 6.563A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 29 removed outlier: 7.279A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 151 through 154 removed outlier: 6.677A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 144 through 147 removed outlier: 3.981A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.392A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.547A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.384A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.735A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 144 through 146 removed outlier: 3.874A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.489A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.505A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 71 removed outlier: 8.490A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 151 through 154 removed outlier: 5.314A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 266 through 270 removed outlier: 3.731A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 539 through 543 removed outlier: 3.624A pdb=" N ILE F 540 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.30 Time building geometry restraints manager: 3.73 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: 11953 1.34 - 1.46: 6705 1.46 - 1.58: 16581 1.58 - 1.70: 43 1.70 - 1.82: 284 Bond restraints: 35566 Sorted by residual: bond pdb=" C ALA D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 1.332 1.387 -0.055 1.12e-02 7.97e+03 2.37e+01 bond pdb=" CG PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 1.512 1.430 0.082 2.70e-02 1.37e+03 9.30e+00 bond pdb=" CB MET C 427 " pdb=" CG MET C 427 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" CD2 PHE F 771 " pdb=" CE2 PHE F 771 " ideal model delta sigma weight residual 1.382 1.330 0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" CB PHE F 771 " pdb=" CG PHE F 771 " ideal model delta sigma weight residual 1.502 1.466 0.036 2.30e-02 1.89e+03 2.42e+00 ... (remaining 35561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 47418 2.25 - 4.50: 589 4.50 - 6.75: 74 6.75 - 9.00: 7 9.00 - 11.25: 3 Bond angle restraints: 48091 Sorted by residual: angle pdb=" N PRO A 170 " pdb=" CD PRO A 170 " pdb=" CG PRO A 170 " ideal model delta sigma weight residual 103.80 96.29 7.51 1.20e+00 6.94e-01 3.91e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 111.50 105.05 6.45 1.40e+00 5.10e-01 2.12e+01 angle pdb=" CA PRO B 298 " pdb=" N PRO B 298 " pdb=" CD PRO B 298 " ideal model delta sigma weight residual 112.00 105.84 6.16 1.40e+00 5.10e-01 1.93e+01 angle pdb=" C PHE B 768 " pdb=" CA PHE B 768 " pdb=" CB PHE B 768 " ideal model delta sigma weight residual 115.79 111.16 4.63 1.19e+00 7.06e-01 1.51e+01 angle pdb=" CB PRO A 170 " pdb=" CG PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 105.40 96.55 8.85 2.30e+00 1.89e-01 1.48e+01 ... (remaining 48086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.91: 21645 31.91 - 63.82: 483 63.82 - 95.73: 67 95.73 - 127.64: 5 127.64 - 159.55: 4 Dihedral angle restraints: 22204 sinusoidal: 9432 harmonic: 12772 Sorted by residual: dihedral pdb=" C5' ADP F 902 " pdb=" O5' ADP F 902 " pdb=" PA ADP F 902 " pdb=" O2A ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 99.56 -159.55 1 2.00e+01 2.50e-03 4.65e+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 90.26 -150.26 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PA ADP F 902 " pdb=" PB ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 85.95 -145.94 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 22201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4005 0.042 - 0.084: 971 0.084 - 0.125: 380 0.125 - 0.167: 47 0.167 - 0.209: 2 Chirality restraints: 5405 Sorted by residual: chirality pdb=" CB ILE A 690 " pdb=" CA ILE A 690 " pdb=" CG1 ILE A 690 " pdb=" CG2 ILE A 690 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE D 151 " pdb=" N ILE D 151 " pdb=" C ILE D 151 " pdb=" CB ILE D 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CB THR F 679 " pdb=" CA THR F 679 " pdb=" OG1 THR F 679 " pdb=" CG2 THR F 679 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 5402 not shown) Planarity restraints: 6298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.090 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO B 298 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " -0.062 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A 170 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 454 " -0.009 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP A 454 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 454 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 454 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 454 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 454 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 454 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 454 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 454 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 454 " 0.002 2.00e-02 2.50e+03 ... (remaining 6295 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 303 2.59 - 3.17: 29941 3.17 - 3.75: 56777 3.75 - 4.32: 79449 4.32 - 4.90: 127993 Nonbonded interactions: 294463 Sorted by model distance: nonbonded pdb=" O1G ATP B 901 " pdb="MG MG B 903 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 903 " model vdw 2.023 2.170 nonbonded pdb=" OG1 THR E 525 " pdb="MG MG E 903 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR B 525 " pdb="MG MG B 903 " model vdw 2.035 2.170 ... (remaining 294458 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 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 535 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 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 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 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 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 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 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) or resid 535 through 545 or resid 558 throu \ gh 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 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 or (resid 338 through 3 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 340 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 533 or (resid 534 and (name N or name \ CA or name C or name O or name CB )) 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.050 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 35566 Z= 0.148 Angle : 0.641 11.248 48091 Z= 0.351 Chirality : 0.043 0.209 5405 Planarity : 0.005 0.133 6298 Dihedral : 13.996 159.554 13914 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.75 % Favored : 98.20 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % 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: 0.89 (0.13), residues: 4391 helix: 1.08 (0.12), residues: 1946 sheet: 0.28 (0.20), residues: 659 loop : 0.35 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 741 TYR 0.014 0.001 TYR D 203 PHE 0.027 0.001 PHE A 360 TRP 0.051 0.002 TRP A 454 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00309 (35566) covalent geometry : angle 0.64075 (48091) hydrogen bonds : bond 0.14845 ( 1608) hydrogen bonds : angle 5.92241 ( 4635) *********************** 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 274 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.9401 time to fit residues: 295.6243 Evaluate side-chains 141 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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: 10.0000 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN D 533 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN F 36 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.099964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.063169 restraints weight = 108267.671| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.77 r_work: 0.2887 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35566 Z= 0.194 Angle : 0.629 15.012 48091 Z= 0.317 Chirality : 0.045 0.157 5405 Planarity : 0.005 0.070 6298 Dihedral : 11.064 170.333 5135 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 0.78 % Allowed : 6.27 % Favored : 92.95 % 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: 1.11 (0.13), residues: 4391 helix: 1.35 (0.12), residues: 1979 sheet: 0.01 (0.19), residues: 675 loop : 0.52 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 711 TYR 0.022 0.002 TYR D 173 PHE 0.024 0.002 PHE F 771 TRP 0.025 0.002 TRP A 476 HIS 0.010 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00453 (35566) covalent geometry : angle 0.62894 (48091) hydrogen bonds : bond 0.04463 ( 1608) hydrogen bonds : angle 4.81312 ( 4635) *********************** 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 177 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 445 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5279 (mp) REVERT: B 508 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8482 (mmm) REVERT: B 740 MET cc_start: 0.8649 (mmm) cc_final: 0.8196 (tpp) REVERT: C 60 LYS cc_start: 0.9045 (mttt) cc_final: 0.8583 (mppt) REVERT: C 173 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: D 41 LEU cc_start: 0.8584 (tp) cc_final: 0.8308 (tp) REVERT: D 46 MET cc_start: 0.7420 (mpp) cc_final: 0.7109 (mpp) REVERT: D 84 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8448 (ptp) REVERT: D 143 TYR cc_start: 0.8153 (m-80) cc_final: 0.7821 (m-10) REVERT: E 84 MET cc_start: 0.7871 (ptp) cc_final: 0.7506 (pmm) REVERT: E 110 TYR cc_start: 0.7408 (m-80) cc_final: 0.7076 (m-80) REVERT: E 678 MET cc_start: 0.9254 (mmp) cc_final: 0.9037 (mmm) REVERT: F 46 MET cc_start: 0.2809 (mmp) cc_final: 0.2604 (mmm) outliers start: 29 outliers final: 5 residues processed: 160 average time/residue: 0.7570 time to fit residues: 143.2756 Evaluate side-chains 147 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 762 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 313 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 370 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 278 optimal weight: 2.9990 chunk 440 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 421 GLN B 533 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN E 50 GLN F 421 GLN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.099768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061923 restraints weight = 108430.074| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.36 r_work: 0.2872 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35566 Z= 0.150 Angle : 0.573 21.754 48091 Z= 0.284 Chirality : 0.044 0.155 5405 Planarity : 0.004 0.076 6298 Dihedral : 10.847 174.159 5135 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 1.05 % Allowed : 7.99 % Favored : 90.97 % 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: 1.30 (0.13), residues: 4391 helix: 1.57 (0.12), residues: 1967 sheet: 0.09 (0.20), residues: 646 loop : 0.53 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 709 TYR 0.016 0.001 TYR D 138 PHE 0.016 0.001 PHE F 771 TRP 0.011 0.001 TRP A 454 HIS 0.009 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00347 (35566) covalent geometry : angle 0.57309 (48091) hydrogen bonds : bond 0.03888 ( 1608) hydrogen bonds : angle 4.48181 ( 4635) *********************** 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 184 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.8185 (mmm) cc_final: 0.7942 (mmm) REVERT: A 550 MET cc_start: 0.8038 (ptm) cc_final: 0.7613 (tpt) REVERT: B 349 ARG cc_start: 0.8320 (tpp-160) cc_final: 0.8057 (tpp-160) REVERT: B 508 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8548 (mmm) REVERT: B 740 MET cc_start: 0.8654 (mmm) cc_final: 0.8370 (tpp) REVERT: C 84 MET cc_start: 0.8889 (mtm) cc_final: 0.8671 (mtp) REVERT: C 173 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: C 219 MET cc_start: 0.8694 (mtt) cc_final: 0.8378 (mtm) REVERT: D 41 LEU cc_start: 0.8573 (tp) cc_final: 0.8330 (tp) REVERT: D 46 MET cc_start: 0.7481 (mpp) cc_final: 0.7122 (mpp) REVERT: E 84 MET cc_start: 0.7957 (ptp) cc_final: 0.7612 (pmm) REVERT: E 110 TYR cc_start: 0.7510 (m-80) cc_final: 0.7173 (m-80) REVERT: E 508 MET cc_start: 0.6371 (mtm) cc_final: 0.5815 (mtt) outliers start: 39 outliers final: 8 residues processed: 165 average time/residue: 0.7353 time to fit residues: 144.0744 Evaluate side-chains 139 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 64 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 406 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 243 optimal weight: 0.5980 chunk 381 optimal weight: 30.0000 chunk 146 optimal weight: 8.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 GLN B 458 GLN D 21 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 538 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.097406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059470 restraints weight = 108048.964| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.83 r_work: 0.2777 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 35566 Z= 0.304 Angle : 0.664 18.318 48091 Z= 0.333 Chirality : 0.047 0.193 5405 Planarity : 0.005 0.062 6298 Dihedral : 11.047 176.522 5135 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 9.38 % Favored : 89.22 % 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: 1.12 (0.13), residues: 4391 helix: 1.41 (0.12), residues: 1962 sheet: 0.02 (0.20), residues: 645 loop : 0.44 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 638 TYR 0.020 0.002 TYR D 173 PHE 0.021 0.002 PHE A 452 TRP 0.019 0.002 TRP A 476 HIS 0.009 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00712 (35566) covalent geometry : angle 0.66406 (48091) hydrogen bonds : bond 0.04421 ( 1608) hydrogen bonds : angle 4.61623 ( 4635) *********************** 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 191 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 139 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8253 (ptm) cc_final: 0.7768 (tpt) REVERT: B 332 MET cc_start: 0.8956 (mmm) cc_final: 0.8716 (mtp) REVERT: B 344 MET cc_start: 0.8022 (ptm) cc_final: 0.7582 (ptp) REVERT: B 349 ARG cc_start: 0.8463 (tpp-160) cc_final: 0.8075 (tpp-160) REVERT: B 452 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8080 (t80) REVERT: B 508 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (mmm) REVERT: B 740 MET cc_start: 0.8667 (mmm) cc_final: 0.8209 (tpp) REVERT: C 173 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: D 20 LYS cc_start: 0.8079 (tptp) cc_final: 0.7875 (tptp) REVERT: D 143 TYR cc_start: 0.8184 (m-80) cc_final: 0.7856 (m-10) REVERT: E 84 MET cc_start: 0.7794 (ptp) cc_final: 0.7484 (pmm) REVERT: E 110 TYR cc_start: 0.7596 (m-80) cc_final: 0.7176 (m-80) REVERT: E 430 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8278 (OUTLIER) REVERT: E 508 MET cc_start: 0.6476 (mtm) cc_final: 0.5899 (mtt) REVERT: E 611 MET cc_start: 0.8722 (tpp) cc_final: 0.8412 (tpp) outliers start: 52 outliers final: 18 residues processed: 177 average time/residue: 0.6910 time to fit residues: 147.4432 Evaluate side-chains 154 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 122 optimal weight: 0.6980 chunk 251 optimal weight: 0.8980 chunk 310 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 430 optimal weight: 20.0000 chunk 433 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 406 HIS C 616 ASN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.097932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060110 restraints weight = 107829.246| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.93 r_work: 0.2824 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35566 Z= 0.200 Angle : 0.590 18.954 48091 Z= 0.294 Chirality : 0.044 0.162 5405 Planarity : 0.004 0.061 6298 Dihedral : 10.790 166.076 5135 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 1.21 % Allowed : 10.43 % Favored : 88.36 % 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: 1.20 (0.13), residues: 4391 helix: 1.52 (0.12), residues: 1962 sheet: -0.05 (0.20), residues: 649 loop : 0.47 (0.15), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 377 TYR 0.018 0.001 TYR D 173 PHE 0.015 0.001 PHE F 771 TRP 0.012 0.001 TRP A 476 HIS 0.009 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00468 (35566) covalent geometry : angle 0.58998 (48091) hydrogen bonds : bond 0.03915 ( 1608) hydrogen bonds : angle 4.42974 ( 4635) *********************** 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 183 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8225 (ptm) cc_final: 0.7775 (tpt) REVERT: B 349 ARG cc_start: 0.8473 (tpp-160) cc_final: 0.8140 (tpp-160) REVERT: B 432 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5559 (tt) REVERT: B 452 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 508 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8743 (mmm) REVERT: B 740 MET cc_start: 0.8660 (mmm) cc_final: 0.8396 (tpp) REVERT: C 84 MET cc_start: 0.8788 (mtm) cc_final: 0.8545 (mtp) REVERT: C 173 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: C 219 MET cc_start: 0.8699 (mtt) cc_final: 0.8435 (mtm) REVERT: D 41 LEU cc_start: 0.8601 (tp) cc_final: 0.8235 (tm) REVERT: D 46 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7703 (mtp) REVERT: D 84 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8629 (ptm) REVERT: D 143 TYR cc_start: 0.8127 (m-80) cc_final: 0.7833 (m-10) REVERT: D 442 MET cc_start: 0.8766 (mmm) cc_final: 0.8540 (mmt) REVERT: E 84 MET cc_start: 0.7823 (ptp) cc_final: 0.7503 (pmm) REVERT: E 110 TYR cc_start: 0.7562 (m-80) cc_final: 0.7119 (m-80) REVERT: E 430 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8284 (tp) REVERT: E 508 MET cc_start: 0.6484 (mtm) cc_final: 0.5921 (mtt) REVERT: E 611 MET cc_start: 0.8709 (tpp) cc_final: 0.8499 (tpp) outliers start: 45 outliers final: 18 residues processed: 167 average time/residue: 0.7301 time to fit residues: 146.6845 Evaluate side-chains 157 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 762 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 72 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 335 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 386 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS D 384 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.097604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059259 restraints weight = 107444.627| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.82 r_work: 0.2819 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 35566 Z= 0.207 Angle : 0.595 17.935 48091 Z= 0.294 Chirality : 0.044 0.172 5405 Planarity : 0.004 0.063 6298 Dihedral : 10.735 152.174 5135 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 1.53 % Allowed : 11.42 % Favored : 87.05 % 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: 1.18 (0.13), residues: 4391 helix: 1.53 (0.12), residues: 1968 sheet: -0.10 (0.20), residues: 648 loop : 0.46 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 89 TYR 0.015 0.001 TYR D 173 PHE 0.013 0.001 PHE A 52 TRP 0.012 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00486 (35566) covalent geometry : angle 0.59477 (48091) hydrogen bonds : bond 0.03884 ( 1608) hydrogen bonds : angle 4.38104 ( 4635) *********************** 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 193 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8200 (ptm) cc_final: 0.7761 (tpt) REVERT: B 344 MET cc_start: 0.8018 (ptm) cc_final: 0.7698 (ptp) REVERT: B 349 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.8022 (tpp-160) REVERT: B 432 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5707 (tt) REVERT: B 452 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 740 MET cc_start: 0.8651 (mmm) cc_final: 0.8163 (tpp) REVERT: C 84 MET cc_start: 0.8673 (mtm) cc_final: 0.8452 (mtp) REVERT: C 173 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: C 219 MET cc_start: 0.8694 (mtt) cc_final: 0.8457 (mtm) REVERT: D 41 LEU cc_start: 0.8652 (tp) cc_final: 0.8323 (tm) REVERT: D 46 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7737 (mtp) REVERT: D 84 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8649 (ptm) REVERT: D 143 TYR cc_start: 0.8129 (m-80) cc_final: 0.7861 (m-10) REVERT: D 442 MET cc_start: 0.8739 (mmm) cc_final: 0.8488 (mmt) REVERT: E 84 MET cc_start: 0.7718 (ptp) cc_final: 0.7318 (pmm) REVERT: E 110 TYR cc_start: 0.7583 (m-10) cc_final: 0.7140 (m-80) REVERT: E 430 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8207 (tp) REVERT: E 508 MET cc_start: 0.6584 (mtm) cc_final: 0.5990 (mtt) REVERT: E 611 MET cc_start: 0.8657 (tpp) cc_final: 0.8278 (tpp) REVERT: F 611 MET cc_start: 0.7697 (mmt) cc_final: 0.7368 (tmm) outliers start: 57 outliers final: 26 residues processed: 175 average time/residue: 0.6660 time to fit residues: 141.7359 Evaluate side-chains 164 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 4 optimal weight: 20.0000 chunk 219 optimal weight: 0.0980 chunk 348 optimal weight: 0.9990 chunk 391 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 29 optimal weight: 0.0870 chunk 427 optimal weight: 0.5980 chunk 337 optimal weight: 0.9990 chunk 432 optimal weight: 7.9990 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.099075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061212 restraints weight = 107284.047| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.63 r_work: 0.2871 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35566 Z= 0.100 Angle : 0.543 18.802 48091 Z= 0.266 Chirality : 0.042 0.147 5405 Planarity : 0.004 0.059 6298 Dihedral : 10.390 156.953 5135 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 1.13 % Allowed : 12.17 % Favored : 86.70 % 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: 1.38 (0.13), residues: 4391 helix: 1.71 (0.12), residues: 1971 sheet: -0.06 (0.20), residues: 635 loop : 0.56 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.013 0.001 TYR D 173 PHE 0.014 0.001 PHE A 152 TRP 0.007 0.001 TRP D 454 HIS 0.009 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00221 (35566) covalent geometry : angle 0.54320 (48091) hydrogen bonds : bond 0.03341 ( 1608) hydrogen bonds : angle 4.15952 ( 4635) *********************** 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: 42 poor density : 139 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8075 (ptm) cc_final: 0.7692 (tpt) REVERT: B 344 MET cc_start: 0.7939 (ptm) cc_final: 0.7642 (ptp) REVERT: B 349 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.8078 (tpp-160) REVERT: B 432 LEU cc_start: 0.6111 (mm) cc_final: 0.5886 (tt) REVERT: B 449 MET cc_start: 0.6410 (tpt) cc_final: 0.6056 (tpp) REVERT: B 452 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 740 MET cc_start: 0.8673 (mmm) cc_final: 0.8136 (tpp) REVERT: C 84 MET cc_start: 0.8657 (mtm) cc_final: 0.8399 (mtp) REVERT: C 173 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7377 (m-80) REVERT: D 41 LEU cc_start: 0.8649 (tp) cc_final: 0.8269 (tm) REVERT: D 46 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7725 (mtp) REVERT: D 60 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8250 (mppt) REVERT: D 84 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8590 (ptm) REVERT: D 442 MET cc_start: 0.8767 (mmm) cc_final: 0.8510 (mmt) REVERT: E 84 MET cc_start: 0.7907 (ptp) cc_final: 0.7583 (pmm) REVERT: E 110 TYR cc_start: 0.7554 (m-10) cc_final: 0.7120 (m-80) REVERT: E 508 MET cc_start: 0.6572 (mtm) cc_final: 0.5993 (mtt) REVERT: E 611 MET cc_start: 0.8625 (tpp) cc_final: 0.8200 (tpp) outliers start: 42 outliers final: 19 residues processed: 170 average time/residue: 0.7019 time to fit residues: 144.2064 Evaluate side-chains 155 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 141 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 439 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 296 optimal weight: 9.9990 chunk 422 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN B 499 HIS C 499 HIS ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.096627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.058484 restraints weight = 108123.066| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.03 r_work: 0.2787 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 35566 Z= 0.310 Angle : 0.671 16.626 48091 Z= 0.331 Chirality : 0.046 0.196 5405 Planarity : 0.005 0.065 6298 Dihedral : 10.738 149.949 5135 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 1.31 % Allowed : 12.60 % Favored : 86.09 % 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: 1.13 (0.13), residues: 4391 helix: 1.49 (0.12), residues: 1965 sheet: -0.16 (0.19), residues: 658 loop : 0.45 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 89 TYR 0.016 0.002 TYR E 755 PHE 0.019 0.002 PHE A 452 TRP 0.021 0.002 TRP B 551 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00725 (35566) covalent geometry : angle 0.67129 (48091) hydrogen bonds : bond 0.04219 ( 1608) hydrogen bonds : angle 4.45177 ( 4635) *********************** 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 180 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8263 (ptm) cc_final: 0.7827 (tpt) REVERT: B 344 MET cc_start: 0.8057 (ptm) cc_final: 0.7683 (ptp) REVERT: B 432 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5853 (tt) REVERT: B 449 MET cc_start: 0.6696 (tpt) cc_final: 0.6322 (tpp) REVERT: B 452 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8141 (t80) REVERT: B 740 MET cc_start: 0.8647 (mmm) cc_final: 0.8357 (tpp) REVERT: C 84 MET cc_start: 0.8671 (mtm) cc_final: 0.8447 (mtp) REVERT: C 173 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7317 (m-80) REVERT: D 46 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: D 143 TYR cc_start: 0.8139 (m-80) cc_final: 0.7849 (m-10) REVERT: E 84 MET cc_start: 0.7569 (ptp) cc_final: 0.7161 (pmm) REVERT: E 110 TYR cc_start: 0.7608 (m-10) cc_final: 0.7143 (m-80) REVERT: E 508 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6074 (mtt) outliers start: 49 outliers final: 27 residues processed: 168 average time/residue: 0.6707 time to fit residues: 136.9975 Evaluate side-chains 159 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 770 SER Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 50 optimal weight: 0.4980 chunk 269 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 410 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 60.0000 chunk 133 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 432 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 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 = 0.4036 r_free = 0.4036 target = 0.098635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060923 restraints weight = 107413.476| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.47 r_work: 0.2876 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35566 Z= 0.110 Angle : 0.577 17.010 48091 Z= 0.281 Chirality : 0.043 0.172 5405 Planarity : 0.004 0.060 6298 Dihedral : 10.305 155.866 5135 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 1.05 % Allowed : 13.06 % Favored : 85.90 % 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: 1.33 (0.13), residues: 4391 helix: 1.66 (0.12), residues: 1976 sheet: -0.10 (0.20), residues: 638 loop : 0.54 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 89 TYR 0.011 0.001 TYR F 517 PHE 0.033 0.001 PHE D 139 TRP 0.008 0.001 TRP D 454 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00247 (35566) covalent geometry : angle 0.57702 (48091) hydrogen bonds : bond 0.03439 ( 1608) hydrogen bonds : angle 4.19427 ( 4635) *********************** 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: 39 poor density : 139 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8060 (ptm) cc_final: 0.7663 (tpt) REVERT: B 344 MET cc_start: 0.7919 (ptm) cc_final: 0.7599 (ptp) REVERT: B 432 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5984 (tt) REVERT: B 449 MET cc_start: 0.6536 (tpt) cc_final: 0.6127 (tpp) REVERT: B 452 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8185 (t80) REVERT: B 740 MET cc_start: 0.8659 (mmm) cc_final: 0.8168 (tpp) REVERT: B 757 MET cc_start: 0.8814 (ttm) cc_final: 0.8573 (tmm) REVERT: C 173 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: D 60 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8305 (mppt) REVERT: D 442 MET cc_start: 0.8801 (mmm) cc_final: 0.8553 (mmt) REVERT: E 84 MET cc_start: 0.7696 (ptp) cc_final: 0.7341 (pmm) REVERT: E 110 TYR cc_start: 0.7569 (m-10) cc_final: 0.7121 (m-80) REVERT: E 508 MET cc_start: 0.6574 (mtm) cc_final: 0.5993 (mtt) outliers start: 39 outliers final: 20 residues processed: 169 average time/residue: 0.6330 time to fit residues: 130.3866 Evaluate side-chains 154 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 177 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 379 optimal weight: 0.0980 chunk 332 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 415 optimal weight: 0.0370 chunk 320 optimal weight: 0.9980 chunk 335 optimal weight: 5.9990 chunk 419 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 78 optimal weight: 50.0000 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 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 = 0.4041 r_free = 0.4041 target = 0.098822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.061322 restraints weight = 107964.825| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.89 r_work: 0.2871 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35566 Z= 0.105 Angle : 0.579 16.377 48091 Z= 0.280 Chirality : 0.043 0.202 5405 Planarity : 0.004 0.061 6298 Dihedral : 10.163 158.822 5135 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 0.80 % Allowed : 13.38 % Favored : 85.82 % 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: 1.39 (0.13), residues: 4391 helix: 1.73 (0.12), residues: 1959 sheet: -0.04 (0.20), residues: 629 loop : 0.54 (0.15), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 89 TYR 0.012 0.001 TYR A 138 PHE 0.022 0.001 PHE A 674 TRP 0.007 0.001 TRP D 454 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00234 (35566) covalent geometry : angle 0.57938 (48091) hydrogen bonds : bond 0.03295 ( 1608) hydrogen bonds : angle 4.13879 ( 4635) ********************** 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 164 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7995 (ttp) cc_final: 0.7349 (ptm) REVERT: A 449 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: A 550 MET cc_start: 0.8028 (ptm) cc_final: 0.7623 (tpt) REVERT: B 211 LYS cc_start: 0.8727 (mmpt) cc_final: 0.8487 (mppt) REVERT: B 344 MET cc_start: 0.7953 (ptm) cc_final: 0.7651 (ptp) REVERT: B 432 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5996 (tt) REVERT: B 449 MET cc_start: 0.6625 (tpt) cc_final: 0.6214 (tpp) REVERT: B 452 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 740 MET cc_start: 0.8680 (mmm) cc_final: 0.8134 (tpp) REVERT: C 84 MET cc_start: 0.8547 (mtp) cc_final: 0.8092 (ttm) REVERT: C 173 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: D 46 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7686 (mtt) REVERT: D 60 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8285 (mppt) REVERT: D 442 MET cc_start: 0.8800 (mmm) cc_final: 0.8577 (mmt) REVERT: E 84 MET cc_start: 0.7734 (ptp) cc_final: 0.7422 (pmm) REVERT: E 110 TYR cc_start: 0.7578 (m-10) cc_final: 0.7122 (m-80) REVERT: E 508 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6077 (mtt) REVERT: E 678 MET cc_start: 0.9291 (mmp) cc_final: 0.9017 (mmm) REVERT: F 611 MET cc_start: 0.7726 (mmm) cc_final: 0.7526 (tpt) REVERT: F 771 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5279 (m-80) outliers start: 30 outliers final: 18 residues processed: 157 average time/residue: 0.7220 time to fit residues: 136.8494 Evaluate side-chains 157 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 452 PHE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 771 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 417 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 303 optimal weight: 30.0000 chunk 318 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.097176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059803 restraints weight = 107748.439| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.20 r_work: 0.2810 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 35566 Z= 0.236 Angle : 0.643 14.979 48091 Z= 0.314 Chirality : 0.045 0.175 5405 Planarity : 0.005 0.062 6298 Dihedral : 10.421 154.295 5135 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 0.94 % Allowed : 13.54 % Favored : 85.52 % 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: 1.29 (0.13), residues: 4391 helix: 1.64 (0.12), residues: 1961 sheet: -0.17 (0.20), residues: 647 loop : 0.55 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 89 TYR 0.026 0.001 TYR D 138 PHE 0.014 0.002 PHE D 139 TRP 0.013 0.001 TRP A 476 HIS 0.008 0.001 HIS F 115 Details of bonding type rmsd covalent geometry : bond 0.00554 (35566) covalent geometry : angle 0.64260 (48091) hydrogen bonds : bond 0.03813 ( 1608) hydrogen bonds : angle 4.31028 ( 4635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11714.25 seconds wall clock time: 199 minutes 52.14 seconds (11992.14 seconds total)