Starting phenix.real_space_refine on Fri Mar 6 22:39:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln4_23448/03_2026/7ln4_23448.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 178 5.16 5 C 21971 2.51 5 N 6227 2.21 5 O 6678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 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: 35094 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5707 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5858 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 40 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: 5862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5862 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 709} Chain breaks: 3 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: "E" Number of atoms: 5796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5796 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 36, 'TRANS': 701} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5531 Classifications: {'peptide': 703} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.29, per 1000 atoms: 0.24 Number of scatterers: 35094 At special positions: 0 Unit cell: (162.989, 171.625, 136.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 32 15.00 Mg 8 11.99 O 6678 8.00 N 6227 7.00 C 21971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 31 sheets defined 51.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 129 through 140 removed outlier: 4.597A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.632A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.422A 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 234 removed outlier: 3.770A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.615A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.642A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.952A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.798A 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 482 through 499 removed outlier: 4.169A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.813A 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 661 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.590A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 714 Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.640A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 767 removed outlier: 3.707A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 767 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.039A 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: 3.749A 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 removed outlier: 3.654A pdb=" N MET B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) No H-bonds generated for '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 333 removed outlier: 3.582A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.569A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 4.330A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.599A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.585A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.856A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.559A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 547 No H-bonds generated for 'chain 'B' and resid 545 through 547' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.559A pdb=" N VAL B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 609 removed outlier: 3.513A pdb=" N ILE B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.889A pdb=" N ILE B 628 " --> pdb=" O ARG B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.657A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 697 Processing helix chain 'B' and resid 698 through 714 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.765A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.846A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 755 " --> pdb=" O ASP B 751 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 129 through 140 removed outlier: 4.573A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix 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: 4.203A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.192A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 280 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.996A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.718A pdb=" N SER C 352 " --> pdb=" O ARG C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.830A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 430 removed outlier: 3.709A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.772A 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: 3.945A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.585A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 548 Processing helix chain 'C' and resid 553 through 569 removed outlier: 3.597A pdb=" N VAL C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 625 through 629 removed outlier: 4.069A pdb=" N ILE C 628 " --> pdb=" O ARG C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.645A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 714 removed outlier: 3.504A pdb=" N ARG C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.821A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 766 removed outlier: 3.668A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 755 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 129 through 140 removed outlier: 4.699A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 190 through 199 removed outlier: 3.605A pdb=" N GLU D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.597A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 4.021A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.064A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.193A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 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: 3.589A 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 463 through 464 No H-bonds generated for 'chain 'D' and resid 463 through 464' Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.720A 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: 4.032A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.679A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 547 No H-bonds generated for 'chain 'D' and resid 545 through 547' Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.519A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 Processing helix chain 'D' and resid 595 through 609 removed outlier: 3.607A pdb=" N ILE D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.689A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.683A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 714 Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.640A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 766 removed outlier: 3.779A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR D 755 " --> pdb=" O ASP D 751 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 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 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.769A 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: 3.849A 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: 3.756A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 271 through 275 removed outlier: 4.373A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 271 through 275' Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.712A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.283A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 339 removed outlier: 3.922A 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: 3.635A 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: 3.531A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 431 removed outlier: 4.418A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.787A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.705A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 548 Processing helix chain 'E' and resid 553 through 568 Processing helix chain 'E' and resid 579 through 582 Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.513A pdb=" N MET E 611 " --> pdb=" O GLU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.777A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.908A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.658A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.751A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.556A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) removed outlier: 3.737A 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 119 through 124 removed outlier: 3.861A pdb=" N GLU F 124 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 190 through 200 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.365A 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: 3.672A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.786A 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: 4.054A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 335 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 388 removed outlier: 4.491A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET F 388 " --> pdb=" O HIS F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.707A 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 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 removed outlier: 3.982A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 559 through 569 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.639A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 611 removed outlier: 3.567A pdb=" N MET F 611 " --> pdb=" O GLU F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.875A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 625 through 629' Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.868A pdb=" N LEU F 634 " --> pdb=" O ASP F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 714 Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.731A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 7.465A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 40 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.177A 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: 5.537A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.548A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.605A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 543 removed outlier: 6.218A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 7.460A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 151 through 154 removed outlier: 5.442A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 147 removed outlier: 3.591A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.209A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 543 removed outlier: 6.595A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.993A 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: 7.491A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 151 through 154 removed outlier: 6.739A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.340A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.308A 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 543 removed outlier: 6.610A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 7.617A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.756A 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: 6.613A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.559A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.414A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.221A 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 543 removed outlier: 6.559A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.041A 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 29 removed outlier: 7.598A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 151 through 154 removed outlier: 5.430A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC6, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.473A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.244A 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 543 removed outlier: 6.543A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.615A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 38 through 41 Processing sheet with id=AD1, first strand: chain 'F' and resid 151 through 154 removed outlier: 3.519A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 144 through 146 removed outlier: 3.957A pdb=" N ARG F 144 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.455A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.197A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 514 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4569 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: 6.90 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 35330 1.57 - 1.92: 339 1.92 - 2.26: 0 2.26 - 2.61: 0 2.61 - 2.96: 1 Bond restraints: 35670 Sorted by residual: bond pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 1.333 2.958 -1.625 1.47e-02 4.63e+03 1.22e+04 bond pdb=" CG PRO E 636 " pdb=" CD PRO E 636 " ideal model delta sigma weight residual 1.503 1.362 0.141 3.40e-02 8.65e+02 1.72e+01 bond pdb=" CB PRO F 461 " pdb=" CG PRO F 461 " ideal model delta sigma weight residual 1.492 1.677 -0.185 5.00e-02 4.00e+02 1.37e+01 bond pdb=" CB PRO E 636 " pdb=" CG PRO E 636 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CG PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 1.503 1.393 0.110 3.40e-02 8.65e+02 1.05e+01 ... (remaining 35665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.90: 48220 8.90 - 17.79: 4 17.79 - 26.69: 2 26.69 - 35.58: 0 35.58 - 44.48: 1 Bond angle restraints: 48227 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 122.83 78.35 44.48 1.35e+00 5.49e-01 1.09e+03 angle pdb=" CA LEU E 464 " pdb=" C LEU E 464 " pdb=" N ARG E 465 " ideal model delta sigma weight residual 116.11 95.46 20.65 1.30e+00 5.92e-01 2.52e+02 angle pdb=" C LEU E 464 " pdb=" N ARG E 465 " pdb=" CA ARG E 465 " ideal model delta sigma weight residual 122.26 97.10 25.16 1.73e+00 3.34e-01 2.11e+02 angle pdb=" CA PRO E 636 " pdb=" N PRO E 636 " pdb=" CD PRO E 636 " ideal model delta sigma weight residual 112.00 94.42 17.58 1.40e+00 5.10e-01 1.58e+02 angle pdb=" CA PRO F 461 " pdb=" N PRO F 461 " pdb=" CD PRO F 461 " ideal model delta sigma weight residual 112.00 95.26 16.74 1.40e+00 5.10e-01 1.43e+02 ... (remaining 48222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 21812 33.37 - 66.74: 393 66.74 - 100.11: 60 100.11 - 133.47: 3 133.47 - 166.84: 4 Dihedral angle restraints: 22272 sinusoidal: 9442 harmonic: 12830 Sorted by residual: dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual 300.00 133.16 166.84 1 2.00e+01 2.50e-03 4.74e+01 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 -60.00 102.15 -162.15 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' ADP B 902 " pdb=" O5' ADP B 902 " pdb=" PA ADP B 902 " pdb=" O2A ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 81.89 -141.89 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4432 0.051 - 0.103: 807 0.103 - 0.154: 191 0.154 - 0.206: 0 0.206 - 0.257: 1 Chirality restraints: 5431 Sorted by residual: chirality pdb=" CA PRO E 636 " pdb=" N PRO E 636 " pdb=" C PRO E 636 " pdb=" CB PRO E 636 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL E 123 " pdb=" CA VAL E 123 " pdb=" CG1 VAL E 123 " pdb=" CG2 VAL E 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 5428 not shown) Planarity restraints: 6311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 464 " 0.186 2.00e-02 2.50e+03 2.72e-01 7.40e+02 pdb=" C LEU E 464 " -0.444 2.00e-02 2.50e+03 pdb=" O LEU E 464 " 0.254 2.00e-02 2.50e+03 pdb=" N ARG E 465 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 635 " -0.106 5.00e-02 4.00e+02 1.44e-01 3.31e+01 pdb=" N PRO E 636 " 0.248 5.00e-02 4.00e+02 pdb=" CA PRO E 636 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 636 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 460 " -0.104 5.00e-02 4.00e+02 1.43e-01 3.28e+01 pdb=" N PRO F 461 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO F 461 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 461 " -0.073 5.00e-02 4.00e+02 ... (remaining 6308 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 259 2.60 - 3.17: 29219 3.17 - 3.75: 54864 3.75 - 4.32: 75869 4.32 - 4.90: 124419 Nonbonded interactions: 284630 Sorted by model distance: nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 904 " model vdw 2.019 2.170 nonbonded pdb=" OG1 THR D 525 " pdb="MG MG D 903 " model vdw 2.045 2.170 nonbonded pdb=" OG1 THR E 252 " pdb="MG MG E 904 " model vdw 2.059 2.170 nonbonded pdb=" O LEU A 548 " pdb=" OG SER A 555 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR C 525 " pdb="MG MG C 903 " model vdw 2.063 2.170 ... (remaining 284625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 5 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'B' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 461 or resid 472 t \ hrough 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 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'D' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'E' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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 through \ 583 or resid 596 through 762)) selection = (chain 'F' and (resid 23 through 24 or (resid 25 and (name N or name CA or name \ C or name O or name CB )) or resid 26 through 202 or (resid 203 and (name N or n \ ame CA or name C or name O or name CB )) or resid 204 through 238 or (resid 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 46 \ 1 or resid 472 through 507 or (resid 508 and (name N or name CA or name C or nam \ e 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: 3.240 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.270 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.009 1.625 35670 Z= 0.601 Angle : 0.651 44.476 48227 Z= 0.378 Chirality : 0.042 0.257 5431 Planarity : 0.006 0.272 6311 Dihedral : 13.673 166.843 13938 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % Favored : 99.79 % 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: 1.49 (0.13), residues: 4386 helix: 1.36 (0.12), residues: 1928 sheet: 1.62 (0.20), residues: 666 loop : 0.48 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 362 TYR 0.022 0.001 TYR F 495 PHE 0.020 0.001 PHE F 575 TRP 0.018 0.002 TRP A 476 HIS 0.008 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00917 (35670) covalent geometry : angle 0.65098 (48227) hydrogen bonds : bond 0.20851 ( 1576) hydrogen bonds : angle 5.96158 ( 4569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.297 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 outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.9140 time to fit residues: 267.7504 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 421 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 ASN B 692 GLN D 43 GLN D 337 GLN E 270 ASN E 327 GLN F 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.120296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068733 restraints weight = 101149.869| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.59 r_work: 0.2693 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35670 Z= 0.271 Angle : 0.648 7.412 48227 Z= 0.331 Chirality : 0.046 0.171 5431 Planarity : 0.005 0.076 6311 Dihedral : 10.576 173.537 5150 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 0.94 % Allowed : 5.33 % Favored : 93.74 % 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: 1.64 (0.13), residues: 4388 helix: 1.63 (0.12), residues: 1962 sheet: 1.18 (0.19), residues: 695 loop : 0.57 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 711 TYR 0.029 0.001 TYR F 143 PHE 0.016 0.002 PHE E 516 TRP 0.023 0.002 TRP A 454 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00634 (35670) covalent geometry : angle 0.64788 (48227) hydrogen bonds : bond 0.05310 ( 1576) hydrogen bonds : angle 4.58934 ( 4569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8884 (mmm) cc_final: 0.8682 (mmm) REVERT: A 740 MET cc_start: 0.7898 (tmm) cc_final: 0.7688 (tmm) REVERT: B 740 MET cc_start: 0.8979 (tpp) cc_final: 0.8744 (tpp) REVERT: C 100 ILE cc_start: 0.8802 (pt) cc_final: 0.8531 (pp) REVERT: D 84 MET cc_start: 0.8845 (ptm) cc_final: 0.8311 (ppp) REVERT: E 388 MET cc_start: 0.8566 (mtt) cc_final: 0.8187 (mtm) REVERT: E 427 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (mmp) REVERT: F 332 MET cc_start: 0.9240 (mmp) cc_final: 0.8879 (mmm) REVERT: F 344 MET cc_start: 0.8405 (pmm) cc_final: 0.8173 (pmm) REVERT: F 442 MET cc_start: 0.9201 (mmm) cc_final: 0.8648 (mpt) REVERT: F 707 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9283 (pp) outliers start: 35 outliers final: 8 residues processed: 172 average time/residue: 0.8827 time to fit residues: 176.8223 Evaluate side-chains 151 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 707 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 345 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 chunk 438 optimal weight: 20.0000 chunk 443 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 413 optimal weight: 5.9990 chunk 424 optimal weight: 40.0000 chunk 93 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 337 GLN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN E 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.119862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068268 restraints weight = 100817.383| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.59 r_work: 0.2703 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 35670 Z= 0.202 Angle : 0.582 7.626 48227 Z= 0.293 Chirality : 0.044 0.153 5431 Planarity : 0.004 0.062 6311 Dihedral : 10.103 159.484 5150 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % Rotamer: Outliers : 0.86 % Allowed : 7.33 % Favored : 91.81 % 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: 1.69 (0.13), residues: 4388 helix: 1.78 (0.12), residues: 1967 sheet: 1.05 (0.19), residues: 690 loop : 0.52 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 711 TYR 0.025 0.001 TYR F 143 PHE 0.016 0.001 PHE B 682 TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00477 (35670) covalent geometry : angle 0.58216 (48227) hydrogen bonds : bond 0.04434 ( 1576) hydrogen bonds : angle 4.29171 ( 4569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: -0.2715 (ttt) cc_final: -0.2922 (ttt) REVERT: A 219 MET cc_start: 0.9296 (mpp) cc_final: 0.9023 (mpp) REVERT: A 740 MET cc_start: 0.8094 (tmm) cc_final: 0.7874 (tmm) REVERT: B 84 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7909 (pp-130) REVERT: B 550 MET cc_start: 0.9091 (ptm) cc_final: 0.8808 (ttp) REVERT: C 84 MET cc_start: 0.8822 (ttp) cc_final: 0.8524 (ttt) REVERT: C 757 MET cc_start: 0.9447 (ttp) cc_final: 0.8852 (tmm) REVERT: D 84 MET cc_start: 0.8988 (ptm) cc_final: 0.8673 (ppp) REVERT: D 100 ILE cc_start: 0.9300 (pt) cc_final: 0.9096 (pp) REVERT: E 84 MET cc_start: 0.8216 (tmm) cc_final: 0.7916 (ppp) REVERT: E 388 MET cc_start: 0.8630 (mtt) cc_final: 0.8279 (mtm) REVERT: E 427 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8506 (mmp) REVERT: F 332 MET cc_start: 0.9326 (mmp) cc_final: 0.8969 (mmm) REVERT: F 344 MET cc_start: 0.8606 (pmm) cc_final: 0.8381 (pmm) REVERT: F 427 MET cc_start: 0.9133 (mmm) cc_final: 0.8882 (tpt) REVERT: F 442 MET cc_start: 0.9314 (mmm) cc_final: 0.8732 (mpt) outliers start: 32 outliers final: 8 residues processed: 164 average time/residue: 0.8147 time to fit residues: 157.7716 Evaluate side-chains 149 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 672 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 263 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 435 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN F 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.119618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068090 restraints weight = 100491.673| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.60 r_work: 0.2705 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35670 Z= 0.166 Angle : 0.562 11.396 48227 Z= 0.280 Chirality : 0.043 0.194 5431 Planarity : 0.004 0.063 6311 Dihedral : 9.717 149.329 5148 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 1.07 % Allowed : 8.43 % Favored : 90.50 % 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: 1.74 (0.13), residues: 4388 helix: 1.87 (0.12), residues: 1969 sheet: 0.97 (0.19), residues: 689 loop : 0.51 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 711 TYR 0.022 0.001 TYR F 143 PHE 0.019 0.001 PHE F 674 TRP 0.012 0.001 TRP A 476 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00389 (35670) covalent geometry : angle 0.56234 (48227) hydrogen bonds : bond 0.03892 ( 1576) hydrogen bonds : angle 4.12699 ( 4569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8989 (mpp) REVERT: A 332 MET cc_start: 0.8886 (mmm) cc_final: 0.8668 (ttp) REVERT: A 740 MET cc_start: 0.8257 (tmm) cc_final: 0.7979 (tmm) REVERT: A 757 MET cc_start: 0.9701 (OUTLIER) cc_final: 0.9216 (tmm) REVERT: B 84 MET cc_start: 0.8008 (tmm) cc_final: 0.7749 (ppp) REVERT: B 475 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 740 MET cc_start: 0.9004 (tpp) cc_final: 0.8794 (tpp) REVERT: C 84 MET cc_start: 0.8763 (ttp) cc_final: 0.8217 (tmm) REVERT: C 475 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8494 (t) REVERT: C 561 GLU cc_start: 0.9114 (tp30) cc_final: 0.8878 (tt0) REVERT: C 740 MET cc_start: 0.9219 (mmm) cc_final: 0.8963 (mmm) REVERT: C 757 MET cc_start: 0.9435 (ttp) cc_final: 0.8847 (tmm) REVERT: D 84 MET cc_start: 0.9050 (ptm) cc_final: 0.8667 (ppp) REVERT: D 158 MET cc_start: 0.6590 (pmm) cc_final: 0.6381 (pmm) REVERT: D 219 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8760 (mpp) REVERT: E 84 MET cc_start: 0.8358 (tmm) cc_final: 0.8130 (ppp) REVERT: E 388 MET cc_start: 0.8646 (mtt) cc_final: 0.8249 (mtm) REVERT: E 427 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: F 219 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8784 (mpm) REVERT: F 332 MET cc_start: 0.9192 (mmp) cc_final: 0.8950 (mmm) REVERT: F 344 MET cc_start: 0.8646 (pmm) cc_final: 0.8419 (pmm) REVERT: F 442 MET cc_start: 0.9334 (mmm) cc_final: 0.8949 (mmm) outliers start: 40 outliers final: 12 residues processed: 170 average time/residue: 0.8036 time to fit residues: 160.7519 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 173 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 376 optimal weight: 30.0000 chunk 248 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 398 optimal weight: 0.8980 chunk 415 optimal weight: 8.9990 chunk 223 optimal weight: 0.3980 chunk 321 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4143 r_free = 0.4143 target = 0.120212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.068911 restraints weight = 100373.542| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.60 r_work: 0.2731 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35670 Z= 0.118 Angle : 0.536 8.838 48227 Z= 0.265 Chirality : 0.042 0.144 5431 Planarity : 0.004 0.060 6311 Dihedral : 9.301 144.090 5148 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 1.04 % Allowed : 9.29 % Favored : 89.67 % 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: 1.81 (0.13), residues: 4388 helix: 1.96 (0.12), residues: 1970 sheet: 0.99 (0.20), residues: 690 loop : 0.52 (0.16), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 711 TYR 0.020 0.001 TYR F 143 PHE 0.014 0.001 PHE F 674 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00271 (35670) covalent geometry : angle 0.53573 (48227) hydrogen bonds : bond 0.03490 ( 1576) hydrogen bonds : angle 3.99625 ( 4569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8924 (mpp) REVERT: A 332 MET cc_start: 0.8943 (mmm) cc_final: 0.8220 (tmm) REVERT: A 740 MET cc_start: 0.8344 (tmm) cc_final: 0.8074 (tmm) REVERT: A 757 MET cc_start: 0.9703 (ttm) cc_final: 0.9216 (tmm) REVERT: B 84 MET cc_start: 0.8001 (tmm) cc_final: 0.7784 (ppp) REVERT: B 475 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8534 (p) REVERT: B 757 MET cc_start: 0.8940 (mmt) cc_final: 0.8737 (mmt) REVERT: C 84 MET cc_start: 0.8772 (ttp) cc_final: 0.8338 (tmm) REVERT: C 475 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8495 (t) REVERT: C 561 GLU cc_start: 0.9119 (tp30) cc_final: 0.8872 (tt0) REVERT: C 757 MET cc_start: 0.9411 (ttp) cc_final: 0.8840 (tmm) REVERT: D 84 MET cc_start: 0.9039 (ptm) cc_final: 0.8654 (ppp) REVERT: D 546 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8691 (mt-10) REVERT: D 757 MET cc_start: 0.9330 (ttm) cc_final: 0.8832 (tmm) REVERT: E 388 MET cc_start: 0.8446 (mtt) cc_final: 0.8027 (mtm) REVERT: E 427 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: F 332 MET cc_start: 0.9196 (mmp) cc_final: 0.8967 (mmm) REVERT: F 344 MET cc_start: 0.8649 (pmm) cc_final: 0.8410 (pmm) REVERT: F 427 MET cc_start: 0.9184 (mmm) cc_final: 0.8923 (tpt) outliers start: 39 outliers final: 13 residues processed: 170 average time/residue: 0.7800 time to fit residues: 157.0982 Evaluate side-chains 155 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 299 optimal weight: 20.0000 chunk 402 optimal weight: 9.9990 chunk 438 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 403 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 314 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 395 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 398 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.117984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066135 restraints weight = 100942.090| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.58 r_work: 0.2647 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 35670 Z= 0.261 Angle : 0.614 9.766 48227 Z= 0.304 Chirality : 0.045 0.201 5431 Planarity : 0.004 0.063 6311 Dihedral : 9.505 141.297 5148 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.87 % Favored : 97.06 % Rotamer: Outliers : 1.10 % Allowed : 10.28 % Favored : 88.62 % 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: 1.64 (0.13), residues: 4388 helix: 1.85 (0.12), residues: 1969 sheet: 0.80 (0.20), residues: 692 loop : 0.44 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 711 TYR 0.018 0.001 TYR F 143 PHE 0.020 0.001 PHE D 131 TRP 0.012 0.001 TRP D 551 HIS 0.006 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00617 (35670) covalent geometry : angle 0.61430 (48227) hydrogen bonds : bond 0.04203 ( 1576) hydrogen bonds : angle 4.20405 ( 4569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8957 (mpp) REVERT: A 332 MET cc_start: 0.8984 (mmm) cc_final: 0.8739 (ttp) REVERT: A 740 MET cc_start: 0.8367 (tmm) cc_final: 0.8135 (tmm) REVERT: A 757 MET cc_start: 0.9714 (ttm) cc_final: 0.9223 (tmm) REVERT: B 475 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 757 MET cc_start: 0.9019 (mmt) cc_final: 0.8752 (mmt) REVERT: C 84 MET cc_start: 0.8792 (ttp) cc_final: 0.8306 (tmm) REVERT: C 110 TYR cc_start: 0.8106 (m-10) cc_final: 0.7859 (m-80) REVERT: C 275 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: C 475 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8585 (t) REVERT: C 740 MET cc_start: 0.9416 (mmm) cc_final: 0.9178 (mmm) REVERT: C 757 MET cc_start: 0.9434 (ttp) cc_final: 0.8865 (tmm) REVERT: D 84 MET cc_start: 0.9034 (ptm) cc_final: 0.8794 (tmm) REVERT: D 561 GLU cc_start: 0.8924 (tt0) cc_final: 0.8429 (tp30) REVERT: D 757 MET cc_start: 0.9325 (ttm) cc_final: 0.8800 (tmm) REVERT: E 388 MET cc_start: 0.8732 (mtt) cc_final: 0.8318 (mtm) REVERT: F 219 MET cc_start: 0.9384 (mtp) cc_final: 0.9080 (mtp) REVERT: F 344 MET cc_start: 0.8616 (pmm) cc_final: 0.8383 (pmm) outliers start: 41 outliers final: 17 residues processed: 169 average time/residue: 0.7679 time to fit residues: 154.1823 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 178 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 203 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067855 restraints weight = 100971.523| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.60 r_work: 0.2780 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35670 Z= 0.122 Angle : 0.555 10.670 48227 Z= 0.272 Chirality : 0.043 0.212 5431 Planarity : 0.004 0.059 6311 Dihedral : 9.170 137.500 5148 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.78 % Allowed : 11.00 % Favored : 88.22 % 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: 1.76 (0.13), residues: 4388 helix: 1.96 (0.12), residues: 1967 sheet: 0.84 (0.20), residues: 688 loop : 0.50 (0.16), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 711 TYR 0.018 0.001 TYR F 143 PHE 0.018 0.001 PHE F 674 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00280 (35670) covalent geometry : angle 0.55503 (48227) hydrogen bonds : bond 0.03507 ( 1576) hydrogen bonds : angle 4.00754 ( 4569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8957 (mpp) REVERT: A 332 MET cc_start: 0.8991 (mmm) cc_final: 0.8262 (tmm) REVERT: A 737 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: A 740 MET cc_start: 0.8461 (tmm) cc_final: 0.8248 (tmm) REVERT: A 757 MET cc_start: 0.9722 (ttm) cc_final: 0.9218 (tmm) REVERT: B 475 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 757 MET cc_start: 0.9010 (mmt) cc_final: 0.8763 (mmt) REVERT: C 84 MET cc_start: 0.8940 (ttp) cc_final: 0.8408 (tmm) REVERT: C 110 TYR cc_start: 0.8169 (m-10) cc_final: 0.7916 (m-80) REVERT: C 475 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8646 (t) REVERT: C 757 MET cc_start: 0.9406 (ttp) cc_final: 0.8848 (tmm) REVERT: D 84 MET cc_start: 0.9160 (ptm) cc_final: 0.8851 (tmm) REVERT: D 546 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8753 (mt-10) REVERT: D 561 GLU cc_start: 0.8949 (tt0) cc_final: 0.8461 (tp30) REVERT: D 757 MET cc_start: 0.9353 (ttm) cc_final: 0.8848 (tmm) REVERT: E 388 MET cc_start: 0.8565 (mtt) cc_final: 0.8120 (mtm) REVERT: F 332 MET cc_start: 0.9108 (tpp) cc_final: 0.8665 (mmm) REVERT: F 344 MET cc_start: 0.8705 (pmm) cc_final: 0.8469 (pmm) REVERT: F 427 MET cc_start: 0.9149 (mmm) cc_final: 0.8927 (tpt) outliers start: 29 outliers final: 12 residues processed: 163 average time/residue: 0.8104 time to fit residues: 155.8934 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain F residue 375 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 324 optimal weight: 0.8980 chunk 333 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 375 optimal weight: 50.0000 chunk 376 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 GLN E 317 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.066760 restraints weight = 100880.898| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.59 r_work: 0.2744 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35670 Z= 0.188 Angle : 0.587 11.970 48227 Z= 0.288 Chirality : 0.044 0.230 5431 Planarity : 0.004 0.069 6311 Dihedral : 9.199 134.492 5148 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.78 % Favored : 97.15 % Rotamer: Outliers : 0.70 % Allowed : 11.46 % Favored : 87.85 % 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: 1.71 (0.13), residues: 4388 helix: 1.92 (0.12), residues: 1962 sheet: 0.79 (0.20), residues: 691 loop : 0.48 (0.16), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 711 TYR 0.018 0.001 TYR F 143 PHE 0.016 0.001 PHE F 674 TRP 0.010 0.001 TRP D 551 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00445 (35670) covalent geometry : angle 0.58688 (48227) hydrogen bonds : bond 0.03728 ( 1576) hydrogen bonds : angle 4.08325 ( 4569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.9000 (mmm) cc_final: 0.8244 (tmm) REVERT: A 737 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 757 MET cc_start: 0.9716 (ttm) cc_final: 0.9193 (tmm) REVERT: B 475 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8759 (p) REVERT: B 740 MET cc_start: 0.8891 (tpp) cc_final: 0.8249 (tmm) REVERT: B 757 MET cc_start: 0.9018 (mmt) cc_final: 0.8794 (mmt) REVERT: C 84 MET cc_start: 0.8910 (ttp) cc_final: 0.8343 (tmm) REVERT: C 110 TYR cc_start: 0.8195 (m-10) cc_final: 0.7925 (m-80) REVERT: C 475 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8630 (t) REVERT: C 757 MET cc_start: 0.9403 (ttp) cc_final: 0.8854 (tmm) REVERT: D 64 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8260 (mtm-85) REVERT: D 84 MET cc_start: 0.9115 (ptm) cc_final: 0.8797 (tmm) REVERT: D 134 TYR cc_start: 0.8275 (m-80) cc_final: 0.7989 (m-80) REVERT: D 561 GLU cc_start: 0.8955 (tt0) cc_final: 0.8460 (tp30) REVERT: D 757 MET cc_start: 0.9341 (ttm) cc_final: 0.8820 (tmm) REVERT: F 332 MET cc_start: 0.9109 (tpp) cc_final: 0.8823 (mmm) REVERT: F 344 MET cc_start: 0.8689 (pmm) cc_final: 0.8459 (pmm) REVERT: F 740 MET cc_start: 0.9412 (ppp) cc_final: 0.9199 (ptp) outliers start: 26 outliers final: 13 residues processed: 162 average time/residue: 0.8123 time to fit residues: 154.7158 Evaluate side-chains 156 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 375 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 135 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 414 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 426 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 360 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.119516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.068417 restraints weight = 100528.954| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.60 r_work: 0.2781 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 35670 Z= 0.111 Angle : 0.571 12.521 48227 Z= 0.278 Chirality : 0.043 0.227 5431 Planarity : 0.004 0.070 6311 Dihedral : 8.918 128.593 5148 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 0.59 % Allowed : 11.62 % Favored : 87.79 % 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: 1.82 (0.13), residues: 4388 helix: 2.03 (0.12), residues: 1943 sheet: 0.89 (0.20), residues: 679 loop : 0.53 (0.16), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 711 TYR 0.018 0.001 TYR F 143 PHE 0.016 0.001 PHE F 674 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00255 (35670) covalent geometry : angle 0.57120 (48227) hydrogen bonds : bond 0.03276 ( 1576) hydrogen bonds : angle 3.96627 ( 4569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9540 (mtm) cc_final: 0.9283 (mpt) REVERT: A 332 MET cc_start: 0.9006 (mmm) cc_final: 0.8299 (tmm) REVERT: A 449 MET cc_start: 0.8589 (tmm) cc_final: 0.7987 (tpp) REVERT: A 757 MET cc_start: 0.9720 (ttm) cc_final: 0.9210 (tmm) REVERT: B 46 MET cc_start: 0.2536 (ptp) cc_final: 0.2307 (pmm) REVERT: B 427 MET cc_start: 0.8834 (ppp) cc_final: 0.8363 (ppp) REVERT: B 475 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8708 (p) REVERT: B 757 MET cc_start: 0.9028 (mmt) cc_final: 0.8769 (mmt) REVERT: C 64 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8085 (mtm110) REVERT: C 84 MET cc_start: 0.8995 (ttp) cc_final: 0.8423 (tmm) REVERT: C 110 TYR cc_start: 0.8216 (m-10) cc_final: 0.7941 (m-80) REVERT: C 475 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 757 MET cc_start: 0.9378 (ttp) cc_final: 0.8862 (tmm) REVERT: D 64 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8279 (mtm-85) REVERT: D 84 MET cc_start: 0.9144 (ptm) cc_final: 0.8767 (ppp) REVERT: D 134 TYR cc_start: 0.8237 (m-80) cc_final: 0.7928 (m-80) REVERT: D 757 MET cc_start: 0.9354 (ttm) cc_final: 0.8812 (tmm) REVERT: F 332 MET cc_start: 0.9067 (tpp) cc_final: 0.8782 (mmm) REVERT: F 344 MET cc_start: 0.8682 (pmm) cc_final: 0.8441 (pmm) REVERT: F 740 MET cc_start: 0.9401 (ppp) cc_final: 0.9172 (ptp) outliers start: 22 outliers final: 13 residues processed: 161 average time/residue: 0.8270 time to fit residues: 155.9070 Evaluate side-chains 152 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain F residue 375 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 442 optimal weight: 10.0000 chunk 287 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 160 optimal weight: 0.9980 chunk 418 optimal weight: 7.9990 chunk 284 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 406 HIS F 660 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.119734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.068735 restraints weight = 100538.389| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.61 r_work: 0.2789 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 35670 Z= 0.106 Angle : 0.579 13.481 48227 Z= 0.281 Chirality : 0.042 0.243 5431 Planarity : 0.004 0.075 6311 Dihedral : 8.792 125.283 5148 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 0.56 % Allowed : 11.91 % Favored : 87.53 % 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: 1.85 (0.13), residues: 4388 helix: 2.03 (0.12), residues: 1955 sheet: 0.90 (0.20), residues: 679 loop : 0.58 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 711 TYR 0.018 0.001 TYR F 143 PHE 0.018 0.001 PHE F 674 TRP 0.008 0.001 TRP D 551 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00244 (35670) covalent geometry : angle 0.57914 (48227) hydrogen bonds : bond 0.03174 ( 1576) hydrogen bonds : angle 3.94927 ( 4569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9513 (mtm) cc_final: 0.9270 (mpt) REVERT: A 332 MET cc_start: 0.8981 (mmm) cc_final: 0.8284 (tmm) REVERT: A 449 MET cc_start: 0.8586 (tmm) cc_final: 0.7993 (tpp) REVERT: A 737 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: A 757 MET cc_start: 0.9717 (ttm) cc_final: 0.9214 (tmm) REVERT: B 46 MET cc_start: 0.2578 (ptp) cc_final: 0.2359 (pmm) REVERT: B 475 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 740 MET cc_start: 0.8771 (tpp) cc_final: 0.8070 (tmm) REVERT: C 64 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8156 (mtm110) REVERT: C 84 MET cc_start: 0.8979 (ttp) cc_final: 0.8163 (tmm) REVERT: C 110 TYR cc_start: 0.8214 (m-10) cc_final: 0.7932 (m-80) REVERT: C 475 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8560 (t) REVERT: C 757 MET cc_start: 0.9395 (ttp) cc_final: 0.8907 (tmm) REVERT: D 64 ARG cc_start: 0.8752 (mtp85) cc_final: 0.8305 (mtm-85) REVERT: D 84 MET cc_start: 0.9155 (ptm) cc_final: 0.8778 (ppp) REVERT: D 134 TYR cc_start: 0.8349 (m-80) cc_final: 0.8030 (m-80) REVERT: D 757 MET cc_start: 0.9362 (ttm) cc_final: 0.8844 (tmm) REVERT: F 158 MET cc_start: 0.6414 (mpp) cc_final: 0.5195 (tmt) REVERT: F 332 MET cc_start: 0.9048 (tpp) cc_final: 0.8816 (mmm) REVERT: F 344 MET cc_start: 0.8679 (pmm) cc_final: 0.8435 (pmm) REVERT: F 740 MET cc_start: 0.9425 (ppp) cc_final: 0.9158 (ptp) outliers start: 21 outliers final: 13 residues processed: 155 average time/residue: 0.8311 time to fit residues: 151.2401 Evaluate side-chains 151 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 375 THR Chi-restraints excluded: chain F residue 388 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 242 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 431 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 387 optimal weight: 40.0000 chunk 403 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 603 GLN F 406 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.119122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067914 restraints weight = 100693.263| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.61 r_work: 0.2771 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35670 Z= 0.146 Angle : 0.590 12.430 48227 Z= 0.287 Chirality : 0.043 0.235 5431 Planarity : 0.004 0.060 6311 Dihedral : 8.809 124.404 5148 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 0.51 % Allowed : 12.18 % Favored : 87.31 % 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: 1.83 (0.13), residues: 4388 helix: 2.02 (0.12), residues: 1949 sheet: 0.89 (0.20), residues: 679 loop : 0.54 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 708 TYR 0.018 0.001 TYR F 143 PHE 0.018 0.001 PHE F 674 TRP 0.008 0.001 TRP D 551 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00345 (35670) covalent geometry : angle 0.59011 (48227) hydrogen bonds : bond 0.03360 ( 1576) hydrogen bonds : angle 3.98851 ( 4569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13507.62 seconds wall clock time: 229 minutes 37.11 seconds (13777.11 seconds total)