Starting phenix.real_space_refine on Fri Mar 6 22:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln5_23449/03_2026/7ln5_23449.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21949 2.51 5 N 6220 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 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: 35051 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: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5784 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 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: 2 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: 5878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5878 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 702} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 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': 4, 'PTRANS': 37, '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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 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: 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: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.66, per 1000 atoms: 0.25 Number of scatterers: 35051 At special positions: 0 Unit cell: (163.702, 172.206, 137.127, 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 31 15.00 Mg 7 11.99 O 6666 8.00 N 6220 7.00 C 21949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 30 sheets defined 52.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.345A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.988A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.599A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.619A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 335 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.883A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.223A 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 506 removed outlier: 3.681A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.521A pdb=" N ALA A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.800A 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: 4.161A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.789A 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 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.846A 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 139 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.582A 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: 3.840A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.171A 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: 3.987A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 318 through 336 removed outlier: 3.956A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 430 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.675A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) 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: 4.042A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.570A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.556A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 625 through 629 removed outlier: 4.051A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.839A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 741 removed outlier: 4.061A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.526A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 758 " --> pdb=" O LYS B 754 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 removed outlier: 4.411A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.572A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.668A pdb=" N GLU C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.386A 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: 3.840A 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: 4.274A 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: 3.906A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.595A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.864A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.621A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 428 removed outlier: 3.796A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.598A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.955A 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 543 through 548 removed outlier: 4.227A pdb=" N LEU C 547 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 578 through 583 removed outlier: 4.173A 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 649 through 661 removed outlier: 3.517A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) 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 removed outlier: 3.637A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.650A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 767 " --> pdb=" O GLN C 763 " (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: 3.716A 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 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 234 removed outlier: 4.150A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.156A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.524A pdb=" N THR D 316 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.550A 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 354 through 358 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.504A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.619A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.829A 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: 3.738A pdb=" N GLU D 546 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 543 through 547' Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.655A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 4.096A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 609 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.694A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 removed outlier: 3.552A pdb=" N GLU D 712 " --> pdb=" O ARG D 708 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.550A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 removed outlier: 3.732A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.870A 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 139 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.570A pdb=" N GLU E 194 " --> pdb=" O LYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.342A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.882A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (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 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 338 removed outlier: 3.670A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.584A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.629A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 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 506 removed outlier: 4.341A 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: 4.035A pdb=" N LEU E 547 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 569 removed outlier: 3.507A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 582 Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.878A pdb=" N ILE E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.624A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.509A pdb=" N ARG E 635 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.501A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.538A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.580A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR E 755 " --> pdb=" O ASP E 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' 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 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.593A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.551A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.839A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.635A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.673A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.900A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.685A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.535A 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 507 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.593A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.647A pdb=" N ASN F 602 " --> pdb=" O ASP F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.643A 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 removed outlier: 3.577A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.574A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.455A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 154 removed outlier: 3.530A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 114 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 268 removed outlier: 5.861A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.786A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.952A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 109 through 110 removed outlier: 7.230A pdb=" N LYS B 109 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 144 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 154 removed outlier: 3.545A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.655A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.784A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.168A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 150 through 154 removed outlier: 3.893A pdb=" N ASP C 150 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 114 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 146 removed outlier: 4.123A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.351A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.607A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.578A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.683A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 146 removed outlier: 3.806A pdb=" N ARG D 144 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.355A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.726A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 30 removed outlier: 7.171A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 83 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER E 40 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 67 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 109 through 110 removed outlier: 7.281A pdb=" N LYS E 109 " --> pdb=" O ILE E 175 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.990A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.496A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.722A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.386A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 83 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 40 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 109 through 110 removed outlier: 7.129A pdb=" N LYS F 109 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 151 through 154 removed outlier: 5.287A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 114 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL F 116 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.542A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.344A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1584 hydrogen bonds defined for protein. 4557 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: 8.37 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.58: 35297 1.58 - 1.93: 334 1.93 - 2.28: 0 2.28 - 2.64: 0 2.64 - 2.99: 2 Bond restraints: 35633 Sorted by residual: bond pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 1.332 2.990 -1.658 1.52e-02 4.33e+03 1.19e+04 bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.333 2.932 -1.599 1.56e-02 4.11e+03 1.05e+04 bond pdb=" CB PRO C 774 " pdb=" CG PRO C 774 " ideal model delta sigma weight residual 1.492 1.622 -0.130 5.00e-02 4.00e+02 6.76e+00 bond pdb=" CB PRO A 298 " pdb=" CG PRO A 298 " ideal model delta sigma weight residual 1.506 1.575 -0.069 3.90e-02 6.57e+02 3.13e+00 bond pdb=" CG MET C 275 " pdb=" SD MET C 275 " ideal model delta sigma weight residual 1.803 1.761 0.042 2.50e-02 1.60e+03 2.86e+00 ... (remaining 35628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.67: 48159 6.67 - 13.34: 15 13.34 - 20.01: 1 20.01 - 26.68: 2 26.68 - 33.35: 2 Bond angle restraints: 48179 Sorted by residual: angle pdb=" O LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 122.37 89.02 33.35 1.28e+00 6.10e-01 6.79e+02 angle pdb=" C LEU D 464 " pdb=" N ARG D 465 " pdb=" CA ARG D 465 " ideal model delta sigma weight residual 121.94 91.39 30.55 2.00e+00 2.50e-01 2.33e+02 angle pdb=" C LEU E 464 " pdb=" N ARG E 465 " pdb=" CA ARG E 465 " ideal model delta sigma weight residual 121.52 95.53 25.99 2.34e+00 1.83e-01 1.23e+02 angle pdb=" O LEU D 464 " pdb=" C LEU D 464 " pdb=" N ARG D 465 " ideal model delta sigma weight residual 122.06 96.96 25.10 3.24e+00 9.53e-02 6.00e+01 angle pdb=" CA PRO C 774 " pdb=" N PRO C 774 " pdb=" CD PRO C 774 " ideal model delta sigma weight residual 112.00 103.14 8.86 1.40e+00 5.10e-01 4.00e+01 ... (remaining 48174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 21605 33.06 - 66.11: 510 66.11 - 99.17: 96 99.17 - 132.22: 7 132.22 - 165.28: 3 Dihedral angle restraints: 22221 sinusoidal: 9412 harmonic: 12809 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 -60.00 105.28 -165.28 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 94.87 -154.86 1 2.00e+01 2.50e-03 4.57e+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 86.24 -146.24 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 22218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3647 0.032 - 0.063: 1056 0.063 - 0.095: 451 0.095 - 0.127: 251 0.127 - 0.158: 14 Chirality restraints: 5419 Sorted by residual: chirality pdb=" CA THR E 613 " pdb=" N THR E 613 " pdb=" C THR E 613 " pdb=" CB THR E 613 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA PHE D 768 " pdb=" N PHE D 768 " pdb=" C PHE D 768 " pdb=" CB PHE D 768 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CB ILE A 206 " pdb=" CA ILE A 206 " pdb=" CG1 ILE A 206 " pdb=" CG2 ILE A 206 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 5416 not shown) Planarity restraints: 6309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.165 2.00e-02 2.50e+03 2.36e-01 5.56e+02 pdb=" C LEU E 464 " -0.397 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.188 2.00e-02 2.50e+03 pdb=" N ARG E 465 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 464 " 0.125 2.00e-02 2.50e+03 1.75e-01 3.07e+02 pdb=" C LEU D 464 " -0.298 2.00e-02 2.50e+03 pdb=" O LEU D 464 " 0.127 2.00e-02 2.50e+03 pdb=" N ARG D 465 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 773 " 0.087 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO C 774 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " 0.066 5.00e-02 4.00e+02 ... (remaining 6306 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 278 2.59 - 3.17: 29150 3.17 - 3.74: 56289 3.74 - 4.32: 78372 4.32 - 4.90: 126963 Nonbonded interactions: 291052 Sorted by model distance: nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.010 2.170 nonbonded pdb=" O LEU A 548 " pdb=" OG SER A 555 " model vdw 2.037 3.040 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 903 " model vdw 2.041 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 2.045 2.170 nonbonded pdb=" O1G ATP E 902 " pdb="MG MG E 903 " model vdw 2.057 2.170 ... (remaining 291047 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: 2.070 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 33.980 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.013 1.658 35633 Z= 0.804 Angle : 0.670 33.352 48179 Z= 0.366 Chirality : 0.041 0.158 5419 Planarity : 0.006 0.236 6309 Dihedral : 15.268 165.277 13905 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.09 (0.12), residues: 4383 helix: 1.09 (0.12), residues: 1954 sheet: 0.79 (0.20), residues: 639 loop : 0.48 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 323 TYR 0.021 0.001 TYR A 755 PHE 0.021 0.001 PHE A 266 TRP 0.011 0.001 TRP D 551 HIS 0.008 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.01251 (35633) covalent geometry : angle 0.66973 (48179) hydrogen bonds : bond 0.20167 ( 1584) hydrogen bonds : angle 6.28866 ( 4557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 309 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.2357 (mpp) cc_final: 0.1711 (mmp) REVERT: A 357 LEU cc_start: 0.7052 (mt) cc_final: 0.6718 (mt) REVERT: F 84 MET cc_start: 0.4420 (tpt) cc_final: 0.4185 (tpt) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.2734 time to fit residues: 128.4984 Evaluate side-chains 179 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN B 215 GLN B 348 ASN B 568 GLN D 91 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 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 = 0.3962 r_free = 0.3962 target = 0.099405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.061255 restraints weight = 107189.862| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.96 r_work: 0.2803 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35633 Z= 0.187 Angle : 0.625 9.476 48179 Z= 0.314 Chirality : 0.045 0.177 5419 Planarity : 0.005 0.080 6309 Dihedral : 10.685 162.577 5123 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.48 % Allowed : 4.66 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.50 (0.13), residues: 4387 helix: 1.58 (0.12), residues: 1971 sheet: 0.57 (0.20), residues: 645 loop : 0.67 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 711 TYR 0.016 0.002 TYR C 173 PHE 0.016 0.001 PHE A 363 TRP 0.024 0.002 TRP A 476 HIS 0.010 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00434 (35633) covalent geometry : angle 0.62498 (48179) hydrogen bonds : bond 0.04755 ( 1584) hydrogen bonds : angle 4.69810 ( 4557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 115 HIS cc_start: 0.6385 (t70) cc_final: 0.5241 (m170) REVERT: B 314 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 740 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7991 (tmm) REVERT: D 195 GLU cc_start: 0.8992 (tt0) cc_final: 0.8730 (pt0) REVERT: E 46 MET cc_start: 0.7631 (mmt) cc_final: 0.6145 (mpp) REVERT: E 173 TYR cc_start: 0.6646 (m-80) cc_final: 0.6390 (m-80) REVERT: E 442 MET cc_start: 0.8848 (mmm) cc_final: 0.8471 (mpp) REVERT: E 546 GLU cc_start: 0.8880 (pt0) cc_final: 0.8637 (pt0) REVERT: E 561 GLU cc_start: 0.8991 (tp30) cc_final: 0.8660 (tp30) REVERT: E 614 LYS cc_start: 0.9356 (mmtm) cc_final: 0.9143 (mmtm) REVERT: F 219 MET cc_start: 0.9021 (mtp) cc_final: 0.8374 (mtt) REVERT: F 332 MET cc_start: 0.9059 (mmm) cc_final: 0.8640 (mmm) REVERT: F 442 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8421 (tpp) REVERT: F 740 MET cc_start: 0.7596 (tpp) cc_final: 0.7320 (tpt) outliers start: 18 outliers final: 8 residues processed: 215 average time/residue: 0.2277 time to fit residues: 79.9024 Evaluate side-chains 177 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 442 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 96 optimal weight: 9.9990 chunk 74 optimal weight: 0.0270 chunk 331 optimal weight: 0.7980 chunk 245 optimal weight: 0.7980 chunk 334 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 320 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 9 optimal weight: 30.0000 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN E 43 GLN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.099287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059640 restraints weight = 107381.982| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.30 r_work: 0.2863 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35633 Z= 0.139 Angle : 0.556 8.871 48179 Z= 0.276 Chirality : 0.043 0.189 5419 Planarity : 0.004 0.099 6309 Dihedral : 10.412 160.599 5123 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.70 % Allowed : 6.40 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.61 (0.13), residues: 4387 helix: 1.79 (0.12), residues: 1965 sheet: 0.38 (0.19), residues: 660 loop : 0.69 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 53 TYR 0.019 0.001 TYR B 203 PHE 0.013 0.001 PHE B 363 TRP 0.023 0.001 TRP A 476 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00318 (35633) covalent geometry : angle 0.55597 (48179) hydrogen bonds : bond 0.04079 ( 1584) hydrogen bonds : angle 4.39833 ( 4557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.7799 (mmtm) cc_final: 0.7533 (mppt) REVERT: B 115 HIS cc_start: 0.6317 (t70) cc_final: 0.5135 (m170) REVERT: B 314 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 740 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: D 195 GLU cc_start: 0.8946 (tt0) cc_final: 0.8642 (pt0) REVERT: D 449 MET cc_start: 0.9146 (tpt) cc_final: 0.8808 (tpt) REVERT: E 46 MET cc_start: 0.7432 (mmt) cc_final: 0.7221 (mmt) REVERT: E 173 TYR cc_start: 0.6904 (m-80) cc_final: 0.6482 (m-80) REVERT: E 442 MET cc_start: 0.8887 (mmm) cc_final: 0.8487 (mpp) REVERT: E 546 GLU cc_start: 0.8855 (pt0) cc_final: 0.8496 (pt0) REVERT: E 561 GLU cc_start: 0.8958 (tp30) cc_final: 0.8525 (tp30) REVERT: E 614 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9054 (mmtm) REVERT: F 291 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8210 (pp20) REVERT: F 442 MET cc_start: 0.8784 (tpt) cc_final: 0.8458 (tpp) REVERT: F 449 MET cc_start: 0.9025 (tpp) cc_final: 0.8520 (tpp) REVERT: F 505 LYS cc_start: 0.7917 (tttt) cc_final: 0.7599 (ptmm) REVERT: F 740 MET cc_start: 0.7410 (tpp) cc_final: 0.7122 (tpt) outliers start: 26 outliers final: 12 residues processed: 200 average time/residue: 0.2147 time to fit residues: 71.8664 Evaluate side-chains 182 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 291 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 186 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 88 optimal weight: 0.0670 chunk 141 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 chunk 411 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.099318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059885 restraints weight = 106880.399| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.29 r_work: 0.2870 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 35633 Z= 0.120 Angle : 0.530 9.835 48179 Z= 0.261 Chirality : 0.043 0.159 5419 Planarity : 0.004 0.057 6309 Dihedral : 10.218 159.570 5123 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.78 % Allowed : 7.53 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.66 (0.13), residues: 4387 helix: 1.90 (0.12), residues: 1965 sheet: 0.34 (0.20), residues: 650 loop : 0.64 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.018 0.001 TYR B 203 PHE 0.009 0.001 PHE E 302 TRP 0.028 0.001 TRP A 476 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00273 (35633) covalent geometry : angle 0.53009 (48179) hydrogen bonds : bond 0.03631 ( 1584) hydrogen bonds : angle 4.22745 ( 4557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.7415 (mpp) cc_final: 0.7134 (mpp) REVERT: B 60 LYS cc_start: 0.7756 (mmtm) cc_final: 0.7513 (mppt) REVERT: B 84 MET cc_start: 0.6537 (ptp) cc_final: 0.5949 (ptp) REVERT: B 115 HIS cc_start: 0.6305 (t70) cc_final: 0.5103 (m170) REVERT: B 314 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 678 MET cc_start: 0.9146 (mmm) cc_final: 0.8905 (mmp) REVERT: B 740 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: C 275 MET cc_start: 0.8079 (ttm) cc_final: 0.7809 (ttm) REVERT: D 148 LYS cc_start: 0.9198 (tttt) cc_final: 0.8965 (tppt) REVERT: D 195 GLU cc_start: 0.8955 (tt0) cc_final: 0.8713 (pt0) REVERT: D 449 MET cc_start: 0.9148 (tpt) cc_final: 0.8834 (tpt) REVERT: E 46 MET cc_start: 0.7493 (mmt) cc_final: 0.6632 (mmt) REVERT: E 53 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6202 (mmp80) REVERT: E 173 TYR cc_start: 0.6959 (m-80) cc_final: 0.6638 (m-80) REVERT: E 442 MET cc_start: 0.8883 (mmm) cc_final: 0.8457 (mpp) REVERT: E 546 GLU cc_start: 0.8877 (pt0) cc_final: 0.8442 (pt0) REVERT: E 561 GLU cc_start: 0.8993 (tp30) cc_final: 0.8528 (tp30) REVERT: E 614 LYS cc_start: 0.9332 (mmtm) cc_final: 0.8999 (mmtm) REVERT: E 740 MET cc_start: 0.9412 (mmm) cc_final: 0.9211 (tpp) REVERT: F 332 MET cc_start: 0.9050 (mmm) cc_final: 0.8671 (mmm) REVERT: F 442 MET cc_start: 0.8764 (tpt) cc_final: 0.8446 (tpp) REVERT: F 449 MET cc_start: 0.8992 (tpp) cc_final: 0.8460 (tpp) REVERT: F 505 LYS cc_start: 0.7896 (tttt) cc_final: 0.7582 (ptmm) REVERT: F 740 MET cc_start: 0.7500 (tpp) cc_final: 0.7248 (tpt) outliers start: 29 outliers final: 17 residues processed: 196 average time/residue: 0.2197 time to fit residues: 70.9070 Evaluate side-chains 182 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 238 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 376 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 299 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN B 692 GLN ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN ** E 624 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 = 0.3936 r_free = 0.3936 target = 0.097716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057771 restraints weight = 107484.660| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.25 r_work: 0.2812 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 35633 Z= 0.204 Angle : 0.573 8.786 48179 Z= 0.283 Chirality : 0.044 0.202 5419 Planarity : 0.004 0.055 6309 Dihedral : 10.301 158.223 5123 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.02 % Allowed : 8.31 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.62 (0.13), residues: 4387 helix: 1.88 (0.12), residues: 1970 sheet: 0.30 (0.19), residues: 662 loop : 0.62 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.018 0.001 TYR C 173 PHE 0.013 0.001 PHE F 674 TRP 0.036 0.002 TRP A 476 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00475 (35633) covalent geometry : angle 0.57294 (48179) hydrogen bonds : bond 0.03854 ( 1584) hydrogen bonds : angle 4.27753 ( 4557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.8080 (mtt) cc_final: 0.7772 (mtt) REVERT: B 475 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8288 (p) REVERT: B 740 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8029 (tmm) REVERT: B 757 MET cc_start: 0.8780 (mmm) cc_final: 0.8554 (mmt) REVERT: C 427 MET cc_start: 0.8484 (tpp) cc_final: 0.8207 (tpp) REVERT: D 148 LYS cc_start: 0.9190 (tttt) cc_final: 0.8967 (tppt) REVERT: D 195 GLU cc_start: 0.9015 (tt0) cc_final: 0.8755 (pt0) REVERT: D 449 MET cc_start: 0.9151 (tpt) cc_final: 0.8897 (tpt) REVERT: E 46 MET cc_start: 0.7504 (mmt) cc_final: 0.6756 (mmm) REVERT: E 53 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6154 (mmp80) REVERT: E 139 PHE cc_start: 0.7754 (m-80) cc_final: 0.7388 (m-80) REVERT: E 173 TYR cc_start: 0.7034 (m-80) cc_final: 0.6716 (m-80) REVERT: E 442 MET cc_start: 0.8892 (mmm) cc_final: 0.8442 (mpp) REVERT: E 546 GLU cc_start: 0.8899 (pt0) cc_final: 0.8481 (pt0) REVERT: E 561 GLU cc_start: 0.9040 (tp30) cc_final: 0.8555 (tp30) REVERT: E 614 LYS cc_start: 0.9372 (mmtm) cc_final: 0.8985 (mmtm) REVERT: E 740 MET cc_start: 0.9493 (mmm) cc_final: 0.8709 (tmm) REVERT: F 291 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: F 442 MET cc_start: 0.8765 (tpt) cc_final: 0.8450 (tpp) REVERT: F 449 MET cc_start: 0.8977 (tpp) cc_final: 0.8404 (tpp) REVERT: F 505 LYS cc_start: 0.7906 (tttt) cc_final: 0.7583 (ptmm) REVERT: F 740 MET cc_start: 0.7437 (tpp) cc_final: 0.7118 (tpt) outliers start: 38 outliers final: 23 residues processed: 195 average time/residue: 0.2158 time to fit residues: 70.2906 Evaluate side-chains 188 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 183 optimal weight: 0.3980 chunk 205 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 372 optimal weight: 20.0000 chunk 258 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 337 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN E 226 HIS ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 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 = 0.3939 r_free = 0.3939 target = 0.097915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058172 restraints weight = 106671.624| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.26 r_work: 0.2824 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 35633 Z= 0.158 Angle : 0.548 12.571 48179 Z= 0.268 Chirality : 0.043 0.167 5419 Planarity : 0.004 0.056 6309 Dihedral : 10.203 156.157 5123 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.91 % Allowed : 9.38 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.65 (0.13), residues: 4387 helix: 1.90 (0.12), residues: 1977 sheet: 0.25 (0.20), residues: 640 loop : 0.64 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 732 TYR 0.011 0.001 TYR A 110 PHE 0.011 0.001 PHE F 302 TRP 0.035 0.001 TRP A 476 HIS 0.010 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00367 (35633) covalent geometry : angle 0.54756 (48179) hydrogen bonds : bond 0.03621 ( 1584) hydrogen bonds : angle 4.19036 ( 4557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8013 (m-80) cc_final: 0.7662 (m-80) REVERT: B 46 MET cc_start: 0.3144 (mtt) cc_final: 0.2811 (tpp) REVERT: B 219 MET cc_start: 0.8188 (mtt) cc_final: 0.7903 (mtt) REVERT: B 314 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 449 MET cc_start: 0.8727 (tpt) cc_final: 0.8505 (tpp) REVERT: B 475 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8281 (p) REVERT: B 678 MET cc_start: 0.9161 (mmm) cc_final: 0.8920 (mmp) REVERT: B 740 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.7982 (tmm) REVERT: C 287 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.7818 (mtp85) REVERT: C 427 MET cc_start: 0.8485 (tpp) cc_final: 0.8239 (tpp) REVERT: C 442 MET cc_start: 0.8531 (mmm) cc_final: 0.8022 (mmm) REVERT: C 561 GLU cc_start: 0.9047 (tp30) cc_final: 0.8698 (tp30) REVERT: D 148 LYS cc_start: 0.9188 (tttt) cc_final: 0.8971 (tppt) REVERT: D 195 GLU cc_start: 0.9009 (tt0) cc_final: 0.8750 (pt0) REVERT: D 449 MET cc_start: 0.9138 (tpt) cc_final: 0.8843 (tpt) REVERT: D 611 MET cc_start: 0.8983 (mmm) cc_final: 0.8474 (mmm) REVERT: E 46 MET cc_start: 0.7540 (mmt) cc_final: 0.6585 (mmm) REVERT: E 53 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6292 (mmp80) REVERT: E 139 PHE cc_start: 0.7699 (m-80) cc_final: 0.7300 (m-80) REVERT: E 173 TYR cc_start: 0.7139 (m-80) cc_final: 0.6756 (m-80) REVERT: E 442 MET cc_start: 0.8886 (mmm) cc_final: 0.8418 (mpp) REVERT: E 546 GLU cc_start: 0.8882 (pt0) cc_final: 0.8422 (pt0) REVERT: E 561 GLU cc_start: 0.9034 (tp30) cc_final: 0.8545 (tp30) REVERT: E 614 LYS cc_start: 0.9380 (mmtm) cc_final: 0.9024 (mmtm) REVERT: E 740 MET cc_start: 0.9483 (mmm) cc_final: 0.8703 (tmm) REVERT: F 291 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8144 (pp20) REVERT: F 427 MET cc_start: 0.9125 (tpt) cc_final: 0.8880 (tpt) REVERT: F 442 MET cc_start: 0.8778 (tpt) cc_final: 0.8472 (tpp) REVERT: F 449 MET cc_start: 0.8981 (tpp) cc_final: 0.8537 (tpp) REVERT: F 505 LYS cc_start: 0.7916 (tttt) cc_final: 0.7638 (ptmm) REVERT: F 740 MET cc_start: 0.7358 (tpp) cc_final: 0.7035 (tpt) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 0.2208 time to fit residues: 71.7320 Evaluate side-chains 185 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 361 optimal weight: 5.9990 chunk 413 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 369 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 398 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 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 = 0.3949 r_free = 0.3949 target = 0.098388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058874 restraints weight = 107690.509| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.31 r_work: 0.2839 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35633 Z= 0.118 Angle : 0.530 11.929 48179 Z= 0.259 Chirality : 0.043 0.156 5419 Planarity : 0.004 0.054 6309 Dihedral : 10.032 155.930 5123 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 9.59 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.70 (0.13), residues: 4387 helix: 1.95 (0.12), residues: 1975 sheet: 0.26 (0.19), residues: 680 loop : 0.69 (0.16), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 732 TYR 0.019 0.001 TYR A 244 PHE 0.010 0.001 PHE F 302 TRP 0.033 0.001 TRP A 476 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00269 (35633) covalent geometry : angle 0.53019 (48179) hydrogen bonds : bond 0.03400 ( 1584) hydrogen bonds : angle 4.10822 ( 4557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8074 (m-80) cc_final: 0.7822 (m-80) REVERT: A 388 MET cc_start: 0.7522 (mpp) cc_final: 0.7143 (mpp) REVERT: A 757 MET cc_start: 0.9115 (ptp) cc_final: 0.8890 (ptp) REVERT: B 46 MET cc_start: 0.2998 (OUTLIER) cc_final: 0.2656 (tpp) REVERT: B 314 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 475 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 678 MET cc_start: 0.9200 (mmm) cc_final: 0.8936 (mmp) REVERT: B 740 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8045 (tmm) REVERT: C 287 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.7790 (mtp85) REVERT: C 427 MET cc_start: 0.8476 (tpp) cc_final: 0.8230 (tpp) REVERT: C 442 MET cc_start: 0.8497 (mmm) cc_final: 0.7956 (mmm) REVERT: C 445 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7670 (mt) REVERT: C 561 GLU cc_start: 0.9045 (tp30) cc_final: 0.8680 (tp30) REVERT: D 148 LYS cc_start: 0.9163 (tttt) cc_final: 0.8943 (tppt) REVERT: D 195 GLU cc_start: 0.9008 (tt0) cc_final: 0.8757 (pt0) REVERT: D 449 MET cc_start: 0.9133 (tpt) cc_final: 0.8874 (tpt) REVERT: D 611 MET cc_start: 0.8948 (mmm) cc_final: 0.8450 (mmm) REVERT: E 46 MET cc_start: 0.7170 (mmt) cc_final: 0.6858 (mmm) REVERT: E 139 PHE cc_start: 0.7683 (m-80) cc_final: 0.7322 (m-80) REVERT: E 173 TYR cc_start: 0.7178 (m-80) cc_final: 0.6708 (m-80) REVERT: E 442 MET cc_start: 0.8887 (mmm) cc_final: 0.8416 (mpp) REVERT: E 546 GLU cc_start: 0.8904 (pt0) cc_final: 0.8421 (pt0) REVERT: E 561 GLU cc_start: 0.9028 (tp30) cc_final: 0.8539 (tp30) REVERT: E 614 LYS cc_start: 0.9374 (mmtm) cc_final: 0.9021 (mmtm) REVERT: E 740 MET cc_start: 0.9474 (mmm) cc_final: 0.8736 (tmm) REVERT: F 84 MET cc_start: 0.6948 (tpp) cc_final: 0.6702 (tpp) REVERT: F 275 MET cc_start: 0.9463 (mmm) cc_final: 0.9109 (mmm) REVERT: F 291 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: F 442 MET cc_start: 0.8785 (tpt) cc_final: 0.8485 (tpp) REVERT: F 449 MET cc_start: 0.8978 (tpp) cc_final: 0.8544 (tpp) REVERT: F 505 LYS cc_start: 0.7914 (tttt) cc_final: 0.7638 (ptmm) REVERT: F 740 MET cc_start: 0.7339 (tpp) cc_final: 0.7033 (tpt) outliers start: 36 outliers final: 18 residues processed: 194 average time/residue: 0.2083 time to fit residues: 67.7536 Evaluate side-chains 184 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 237 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 422 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 356 optimal weight: 0.7980 chunk 344 optimal weight: 2.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS E 90 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057116 restraints weight = 108089.785| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.25 r_work: 0.2797 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 35633 Z= 0.209 Angle : 0.593 13.889 48179 Z= 0.288 Chirality : 0.044 0.167 5419 Planarity : 0.004 0.055 6309 Dihedral : 10.146 154.900 5123 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.10 % Allowed : 10.24 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.58 (0.13), residues: 4387 helix: 1.84 (0.12), residues: 1981 sheet: 0.20 (0.19), residues: 685 loop : 0.64 (0.16), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 362 TYR 0.016 0.001 TYR C 173 PHE 0.010 0.001 PHE A 302 TRP 0.051 0.002 TRP A 476 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00488 (35633) covalent geometry : angle 0.59267 (48179) hydrogen bonds : bond 0.03799 ( 1584) hydrogen bonds : angle 4.20920 ( 4557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8107 (m-80) cc_final: 0.7774 (m-80) REVERT: A 388 MET cc_start: 0.7503 (mpp) cc_final: 0.7130 (mpp) REVERT: B 314 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 475 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 740 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: C 287 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: C 442 MET cc_start: 0.8520 (mmm) cc_final: 0.7958 (mmm) REVERT: C 445 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7642 (mt) REVERT: C 561 GLU cc_start: 0.9072 (tp30) cc_final: 0.8723 (tp30) REVERT: D 96 LEU cc_start: 0.8952 (mm) cc_final: 0.8619 (mm) REVERT: D 148 LYS cc_start: 0.9182 (tttt) cc_final: 0.8974 (tppt) REVERT: D 195 GLU cc_start: 0.9033 (tt0) cc_final: 0.8796 (pt0) REVERT: D 449 MET cc_start: 0.9159 (tpt) cc_final: 0.8936 (tpt) REVERT: D 611 MET cc_start: 0.9013 (mmm) cc_final: 0.8589 (mmm) REVERT: E 46 MET cc_start: 0.7404 (mmt) cc_final: 0.7093 (mmm) REVERT: E 49 LEU cc_start: 0.9165 (tt) cc_final: 0.8523 (mp) REVERT: E 84 MET cc_start: 0.8517 (tmm) cc_final: 0.8289 (tmt) REVERT: E 139 PHE cc_start: 0.7692 (m-80) cc_final: 0.7294 (m-80) REVERT: E 173 TYR cc_start: 0.7299 (m-80) cc_final: 0.6735 (m-80) REVERT: E 442 MET cc_start: 0.8895 (mmm) cc_final: 0.8413 (mpp) REVERT: E 546 GLU cc_start: 0.8928 (pt0) cc_final: 0.8460 (pt0) REVERT: E 561 GLU cc_start: 0.9044 (tp30) cc_final: 0.8544 (tp30) REVERT: F 291 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: F 387 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.9179 (m-40) REVERT: F 442 MET cc_start: 0.8792 (tpt) cc_final: 0.8499 (tpp) REVERT: F 449 MET cc_start: 0.8967 (tpp) cc_final: 0.8521 (tpp) REVERT: F 505 LYS cc_start: 0.7921 (tttt) cc_final: 0.7662 (ptmm) REVERT: F 740 MET cc_start: 0.7399 (tpp) cc_final: 0.7097 (tpt) REVERT: F 757 MET cc_start: 0.8705 (mtt) cc_final: 0.8384 (mmm) outliers start: 41 outliers final: 25 residues processed: 197 average time/residue: 0.1986 time to fit residues: 66.6875 Evaluate side-chains 189 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 387 ASN Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 22 optimal weight: 6.9990 chunk 278 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 273 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 405 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.097843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058395 restraints weight = 107004.859| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.27 r_work: 0.2829 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35633 Z= 0.129 Angle : 0.561 13.399 48179 Z= 0.271 Chirality : 0.043 0.179 5419 Planarity : 0.004 0.054 6309 Dihedral : 9.970 154.524 5123 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 10.93 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.62 (0.13), residues: 4387 helix: 1.91 (0.12), residues: 1968 sheet: 0.22 (0.19), residues: 695 loop : 0.61 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 732 TYR 0.022 0.001 TYR A 173 PHE 0.014 0.001 PHE C 139 TRP 0.040 0.001 TRP A 476 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00298 (35633) covalent geometry : angle 0.56058 (48179) hydrogen bonds : bond 0.03451 ( 1584) hydrogen bonds : angle 4.09843 ( 4557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8043 (m-80) cc_final: 0.7732 (m-80) REVERT: A 388 MET cc_start: 0.7495 (mpp) cc_final: 0.7148 (mpp) REVERT: A 678 MET cc_start: 0.7836 (mtt) cc_final: 0.7553 (ptp) REVERT: B 475 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 678 MET cc_start: 0.9169 (mmm) cc_final: 0.8930 (mmp) REVERT: B 740 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8019 (tmm) REVERT: C 287 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.7774 (mtp85) REVERT: C 442 MET cc_start: 0.8572 (mmm) cc_final: 0.7976 (mmm) REVERT: C 445 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7622 (mt) REVERT: D 148 LYS cc_start: 0.9177 (tttt) cc_final: 0.8969 (tppt) REVERT: D 195 GLU cc_start: 0.9008 (tt0) cc_final: 0.8763 (pt0) REVERT: D 449 MET cc_start: 0.9144 (tpt) cc_final: 0.8892 (tpt) REVERT: D 611 MET cc_start: 0.8975 (mmm) cc_final: 0.8598 (mmm) REVERT: E 46 MET cc_start: 0.7311 (mmt) cc_final: 0.7057 (mmm) REVERT: E 49 LEU cc_start: 0.9132 (tt) cc_final: 0.8453 (mp) REVERT: E 139 PHE cc_start: 0.7643 (m-80) cc_final: 0.7273 (m-80) REVERT: E 173 TYR cc_start: 0.7277 (m-80) cc_final: 0.6698 (m-80) REVERT: E 442 MET cc_start: 0.8882 (mmm) cc_final: 0.8395 (mpp) REVERT: E 546 GLU cc_start: 0.8948 (pt0) cc_final: 0.8519 (pt0) REVERT: E 561 GLU cc_start: 0.9041 (tp30) cc_final: 0.8546 (tp30) REVERT: E 740 MET cc_start: 0.9438 (mmm) cc_final: 0.9128 (tpp) REVERT: F 84 MET cc_start: 0.6962 (tpp) cc_final: 0.6744 (tpp) REVERT: F 291 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: F 427 MET cc_start: 0.9128 (tpt) cc_final: 0.8721 (tpt) REVERT: F 442 MET cc_start: 0.8774 (tpt) cc_final: 0.8480 (tpp) REVERT: F 505 LYS cc_start: 0.7900 (tttt) cc_final: 0.7644 (ptmm) REVERT: F 740 MET cc_start: 0.7407 (tpp) cc_final: 0.7086 (tpt) REVERT: F 757 MET cc_start: 0.8653 (mtt) cc_final: 0.8323 (mmm) outliers start: 32 outliers final: 22 residues processed: 183 average time/residue: 0.2097 time to fit residues: 65.4799 Evaluate side-chains 183 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 204 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 333 optimal weight: 0.0570 chunk 300 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 342 optimal weight: 0.0670 chunk 388 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 441 optimal weight: 10.0000 chunk 375 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN ** E 624 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 = 0.3945 r_free = 0.3945 target = 0.098093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058794 restraints weight = 107608.035| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.23 r_work: 0.2844 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35633 Z= 0.119 Angle : 0.555 13.076 48179 Z= 0.267 Chirality : 0.043 0.224 5419 Planarity : 0.004 0.055 6309 Dihedral : 9.868 157.606 5123 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.78 % Allowed : 11.04 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.66 (0.13), residues: 4387 helix: 1.94 (0.12), residues: 1968 sheet: 0.28 (0.19), residues: 695 loop : 0.62 (0.16), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 732 TYR 0.018 0.001 TYR A 173 PHE 0.013 0.001 PHE A 758 TRP 0.027 0.001 TRP A 476 HIS 0.006 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00275 (35633) covalent geometry : angle 0.55454 (48179) hydrogen bonds : bond 0.03316 ( 1584) hydrogen bonds : angle 4.05147 ( 4557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8774 Ramachandran restraints generated. 4387 Oldfield, 0 Emsley, 4387 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: 29 poor density : 162 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.8126 (m-80) cc_final: 0.7828 (m-80) REVERT: A 337 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 388 MET cc_start: 0.7506 (mpp) cc_final: 0.7158 (mpp) REVERT: A 678 MET cc_start: 0.7910 (mtt) cc_final: 0.7624 (ptp) REVERT: B 314 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 475 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8358 (p) REVERT: B 678 MET cc_start: 0.9203 (mmm) cc_final: 0.8957 (mmp) REVERT: C 287 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.7808 (mtp85) REVERT: C 442 MET cc_start: 0.8573 (mmm) cc_final: 0.8011 (mmm) REVERT: D 195 GLU cc_start: 0.9026 (tt0) cc_final: 0.8779 (pt0) REVERT: D 442 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: D 449 MET cc_start: 0.9171 (tpt) cc_final: 0.8882 (tpt) REVERT: E 46 MET cc_start: 0.7344 (mmt) cc_final: 0.7066 (mmm) REVERT: E 49 LEU cc_start: 0.9132 (tt) cc_final: 0.8434 (mp) REVERT: E 139 PHE cc_start: 0.7643 (m-80) cc_final: 0.7275 (m-80) REVERT: E 173 TYR cc_start: 0.7330 (m-80) cc_final: 0.6725 (m-80) REVERT: E 442 MET cc_start: 0.8910 (mmm) cc_final: 0.8430 (mpp) REVERT: E 546 GLU cc_start: 0.8883 (pt0) cc_final: 0.8491 (pt0) REVERT: E 561 GLU cc_start: 0.9041 (tp30) cc_final: 0.8560 (tp30) REVERT: E 740 MET cc_start: 0.9424 (mmm) cc_final: 0.9145 (tpp) REVERT: F 291 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: F 427 MET cc_start: 0.9091 (tpt) cc_final: 0.8590 (tpt) REVERT: F 442 MET cc_start: 0.8742 (tpt) cc_final: 0.8446 (tpp) REVERT: F 505 LYS cc_start: 0.7865 (tttt) cc_final: 0.7631 (ptmm) REVERT: F 740 MET cc_start: 0.7390 (tpp) cc_final: 0.7077 (tpt) REVERT: F 757 MET cc_start: 0.8780 (mtt) cc_final: 0.8433 (mmm) outliers start: 29 outliers final: 21 residues processed: 187 average time/residue: 0.2076 time to fit residues: 66.1761 Evaluate side-chains 181 residues out of total 3783 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 443 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 287 ARG Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 757 MET Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 499 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 366 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 190 optimal weight: 0.4980 chunk 371 optimal weight: 8.9990 chunk 312 optimal weight: 40.0000 chunk 201 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 288 optimal weight: 6.9990 chunk 412 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN ** E 624 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 = 0.3931 r_free = 0.3931 target = 0.097352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057867 restraints weight = 107111.389| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.24 r_work: 0.2817 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35633 Z= 0.164 Angle : 0.580 12.670 48179 Z= 0.280 Chirality : 0.043 0.269 5419 Planarity : 0.004 0.054 6309 Dihedral : 9.923 158.320 5123 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.88 % Allowed : 11.04 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % 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: 1.61 (0.13), residues: 4387 helix: 1.88 (0.12), residues: 1980 sheet: 0.26 (0.19), residues: 695 loop : 0.61 (0.16), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 323 TYR 0.017 0.001 TYR A 173 PHE 0.012 0.001 PHE C 139 TRP 0.031 0.001 TRP A 476 HIS 0.007 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00384 (35633) covalent geometry : angle 0.57965 (48179) hydrogen bonds : bond 0.03479 ( 1584) hydrogen bonds : angle 4.10389 ( 4557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11387.43 seconds wall clock time: 194 minutes 37.96 seconds (11677.96 seconds total)