Starting phenix.real_space_refine on Mon Jul 6 11:45:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln4_23448/07_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_23448/07_2026/7ln4_23448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ln4_23448/07_2026/7ln4_23448.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.03, per 1000 atoms: 0.23 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 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: 8.93 Time building geometry restraints manager: 3.74 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: 21682 33.37 - 66.74: 293 66.74 - 100.11: 42 100.11 - 133.47: 3 133.47 - 166.84: 4 Dihedral angle restraints: 22024 sinusoidal: 9194 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 22021 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 34.180 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 12.717 166.843 13690 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/Z covalent geometry : bond 0.00917 / 0.60 (35670) covalent geometry : angle 0.65098 / 0.38 (48227) hydrogen bonds : bond 0.20851 / 13.90 ( 1576) hydrogen bonds : angle 5.96158 / 4.24 ( 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 : 1.347 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: 0.9097 time to fit residues: 267.1090 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 : 1.332 ------------------------------------------------------------------------------- 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... ** 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 C 538 ASN D 43 GLN D 337 GLN E 270 ASN E 327 GLN F 215 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.120198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.068593 restraints weight = 101048.246| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.60 r_work: 0.2690 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 35670 Z= 0.266 Angle : 0.645 7.342 48227 Z= 0.328 Chirality : 0.046 0.163 5431 Planarity : 0.005 0.078 6311 Dihedral : 7.234 172.021 4902 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 0.91 % Allowed : 5.41 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.13), residues: 4388 helix: 1.59 (0.12), residues: 1962 sheet: 1.17 (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 D 713 TYR 0.027 0.001 TYR F 143 PHE 0.016 0.001 PHE B 682 TRP 0.029 0.002 TRP A 454 HIS 0.005 0.001 HIS C 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.27 (35670) covalent geometry : angle 0.64511 / 0.33 (48227) hydrogen bonds : bond 0.05329 / 3.52 ( 1576) hydrogen bonds : angle 4.55395 / 3.26 ( 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 192 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.200 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 740 MET cc_start: 0.7907 (tmm) cc_final: 0.7698 (tmm) REVERT: B 740 MET cc_start: 0.8979 (tpp) cc_final: 0.8748 (tpp) REVERT: C 100 ILE cc_start: 0.8796 (pt) cc_final: 0.8520 (pp) REVERT: D 84 MET cc_start: 0.8884 (ptm) cc_final: 0.8404 (ppp) REVERT: E 84 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: E 388 MET cc_start: 0.8570 (mtt) cc_final: 0.8215 (mtm) REVERT: E 427 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8442 (mmp) REVERT: F 332 MET cc_start: 0.9221 (mmp) cc_final: 0.8871 (mmm) REVERT: F 344 MET cc_start: 0.8420 (pmm) cc_final: 0.8180 (pmm) REVERT: F 442 MET cc_start: 0.9194 (mmm) cc_final: 0.8633 (mpt) REVERT: F 707 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9292 (pp) outliers start: 34 outliers final: 8 residues processed: 173 average time/residue: 0.8652 time to fit residues: 174.8983 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 84 MET 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: 3.9990 chunk 98 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 438 optimal weight: 20.0000 chunk 443 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 413 optimal weight: 10.0000 chunk 424 optimal weight: 40.0000 chunk 93 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 398 GLN B 43 GLN B 384 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN E 226 HIS F 533 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.117321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065157 restraints weight = 102172.207| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.58 r_work: 0.2613 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 35670 Z= 0.382 Angle : 0.716 8.166 48227 Z= 0.362 Chirality : 0.048 0.199 5431 Planarity : 0.006 0.091 6311 Dihedral : 7.067 152.706 4902 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 1.07 % Allowed : 7.84 % Favored : 91.09 % 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: 1.38 (0.13), residues: 4388 helix: 1.55 (0.12), residues: 1967 sheet: 0.86 (0.19), residues: 697 loop : 0.34 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 711 TYR 0.024 0.002 TYR F 143 PHE 0.023 0.002 PHE B 682 TRP 0.022 0.002 TRP A 476 HIS 0.009 0.002 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.38 (35670) covalent geometry : angle 0.71626 / 0.36 (48227) hydrogen bonds : bond 0.05299 / 3.51 ( 1576) hydrogen bonds : angle 4.58718 / 3.28 ( 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 188 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 1.331 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 332 MET cc_start: 0.8905 (mmm) cc_final: 0.8688 (ttp) REVERT: A 740 MET cc_start: 0.8151 (tmm) cc_final: 0.7927 (tmm) REVERT: A 757 MET cc_start: 0.9367 (tmm) cc_final: 0.9048 (tmm) REVERT: C 84 MET cc_start: 0.8892 (ttp) cc_final: 0.8272 (tmm) REVERT: C 110 TYR cc_start: 0.8041 (m-10) cc_final: 0.7814 (m-80) REVERT: C 275 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8102 (mmm) REVERT: C 757 MET cc_start: 0.9462 (ttp) cc_final: 0.8801 (tmm) REVERT: D 84 MET cc_start: 0.9033 (ptm) cc_final: 0.8729 (ppp) REVERT: D 100 ILE cc_start: 0.9262 (pt) cc_final: 0.9058 (pp) REVERT: D 561 GLU cc_start: 0.9052 (tp30) cc_final: 0.8677 (tp30) REVERT: D 757 MET cc_start: 0.9386 (ttm) cc_final: 0.8821 (tmm) REVERT: E 84 MET cc_start: 0.8052 (tmm) cc_final: 0.7826 (ppp) REVERT: E 388 MET cc_start: 0.8824 (mtt) cc_final: 0.8435 (mtm) REVERT: E 427 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8620 (mmp) REVERT: F 332 MET cc_start: 0.9308 (mmp) cc_final: 0.8837 (mmm) REVERT: F 344 MET cc_start: 0.8630 (pmm) cc_final: 0.8397 (pmm) REVERT: F 442 MET cc_start: 0.9333 (mmm) cc_final: 0.8751 (mpt) outliers start: 40 outliers final: 11 residues processed: 172 average time/residue: 0.8133 time to fit residues: 165.3850 Evaluate side-chains 153 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 702 SER Chi-restraints excluded: chain C residue 275 MET 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 D residue 606 THR 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 F residue 340 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 264 optimal weight: 1.9990 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: 0.9990 chunk 137 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 435 optimal weight: 0.0030 chunk 175 optimal weight: 0.7980 chunk 243 optimal weight: 0.7980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN E 404 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 = 0.119390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068009 restraints weight = 100359.339| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.58 r_work: 0.2699 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 35670 Z= 0.115 Angle : 0.549 8.277 48227 Z= 0.273 Chirality : 0.043 0.147 5431 Planarity : 0.004 0.063 6311 Dihedral : 6.569 148.062 4900 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 0.94 % Allowed : 9.07 % Favored : 89.99 % 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: 1.68 (0.13), residues: 4388 helix: 1.86 (0.12), residues: 1962 sheet: 0.84 (0.20), residues: 690 loop : 0.50 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 86 TYR 0.021 0.001 TYR F 143 PHE 0.014 0.001 PHE B 768 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (35670) covalent geometry : angle 0.54938 / 0.27 (48227) hydrogen bonds : bond 0.03796 / 2.51 ( 1576) hydrogen bonds : angle 4.13403 / 2.96 ( 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 181 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9298 (mpp) cc_final: 0.9023 (mpp) REVERT: A 332 MET cc_start: 0.8944 (mmm) cc_final: 0.8244 (tmm) REVERT: A 740 MET cc_start: 0.8305 (tmm) cc_final: 0.8039 (tmm) REVERT: A 757 MET cc_start: 0.9407 (tmm) cc_final: 0.9068 (tmm) REVERT: B 46 MET cc_start: 0.2249 (OUTLIER) cc_final: 0.1891 (pmm) REVERT: B 475 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 84 MET cc_start: 0.8852 (ttp) cc_final: 0.8353 (tmm) REVERT: C 110 TYR cc_start: 0.8051 (m-10) cc_final: 0.7812 (m-80) REVERT: C 475 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8552 (t) REVERT: C 757 MET cc_start: 0.9444 (ttp) cc_final: 0.8855 (tmm) REVERT: D 84 MET cc_start: 0.9131 (ptm) cc_final: 0.8790 (ppp) REVERT: D 219 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8682 (mpp) REVERT: D 757 MET cc_start: 0.9385 (ttm) cc_final: 0.8814 (tmm) REVERT: E 84 MET cc_start: 0.8202 (tmm) cc_final: 0.7991 (ppp) REVERT: E 388 MET cc_start: 0.8673 (mtt) cc_final: 0.8266 (mtm) REVERT: F 332 MET cc_start: 0.9336 (mmp) cc_final: 0.8784 (mmm) REVERT: F 344 MET cc_start: 0.8626 (pmm) cc_final: 0.8387 (pmm) REVERT: F 427 MET cc_start: 0.9111 (mmm) cc_final: 0.8875 (tpt) REVERT: F 442 MET cc_start: 0.9341 (mmm) cc_final: 0.8972 (mmm) outliers start: 35 outliers final: 7 residues processed: 169 average time/residue: 0.8023 time to fit residues: 160.1414 Evaluate side-chains 147 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.323 ------------------------------------------------------------------------------- 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 B residue 46 MET Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 219 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 173 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 366 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 398 optimal weight: 1.9990 chunk 415 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 321 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 348 ASN F 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.118408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.066763 restraints weight = 100652.556| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.56 r_work: 0.2666 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35670 Z= 0.193 Angle : 0.568 9.350 48227 Z= 0.281 Chirality : 0.043 0.155 5431 Planarity : 0.004 0.062 6311 Dihedral : 6.312 143.258 4900 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 0.94 % Allowed : 10.12 % Favored : 88.95 % 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: 1.86 (0.12), residues: 1968 sheet: 0.76 (0.20), residues: 686 loop : 0.46 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 711 TYR 0.019 0.001 TYR F 143 PHE 0.010 0.001 PHE B 682 TRP 0.011 0.001 TRP D 551 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (35670) covalent geometry : angle 0.56788 / 0.28 (48227) hydrogen bonds : bond 0.03921 / 2.60 ( 1576) hydrogen bonds : angle 4.14197 / 2.97 ( 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 176 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 1.378 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: 0.9337 (OUTLIER) cc_final: 0.8945 (mpp) REVERT: A 332 MET cc_start: 0.8967 (mmm) cc_final: 0.8251 (tmm) REVERT: A 740 MET cc_start: 0.8391 (tmm) cc_final: 0.8139 (tmm) REVERT: A 757 MET cc_start: 0.9436 (tmm) cc_final: 0.9093 (tmm) REVERT: B 475 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 84 MET cc_start: 0.8850 (ttp) cc_final: 0.8235 (tmm) REVERT: C 110 TYR cc_start: 0.8080 (m-10) cc_final: 0.7846 (m-80) REVERT: C 275 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: C 475 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 757 MET cc_start: 0.9437 (ttp) cc_final: 0.8852 (tmm) REVERT: D 84 MET cc_start: 0.9029 (ptm) cc_final: 0.8627 (ppp) REVERT: D 219 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8742 (mpp) REVERT: D 757 MET cc_start: 0.9381 (ttm) cc_final: 0.8809 (tmm) REVERT: E 84 MET cc_start: 0.8337 (tmm) cc_final: 0.8104 (ppp) REVERT: F 344 MET cc_start: 0.8635 (pmm) cc_final: 0.8377 (pmm) outliers start: 35 outliers final: 14 residues processed: 167 average time/residue: 0.7910 time to fit residues: 156.3976 Evaluate side-chains 157 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 219 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 375 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 299 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 438 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 278 optimal weight: 0.8980 chunk 403 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 395 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 HIS C 624 ASN D 43 GLN E 317 HIS F 660 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.117791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065957 restraints weight = 100873.227| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.57 r_work: 0.2721 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35670 Z= 0.231 Angle : 0.593 10.094 48227 Z= 0.293 Chirality : 0.044 0.200 5431 Planarity : 0.004 0.062 6311 Dihedral : 6.257 139.908 4900 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 1.10 % Allowed : 10.73 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.13), residues: 4388 helix: 1.84 (0.12), residues: 1961 sheet: 0.70 (0.20), residues: 693 loop : 0.40 (0.15), residues: 1734 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 0.013 0.001 PHE F 674 TRP 0.011 0.001 TRP D 551 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (35670) covalent geometry : angle 0.59318 / 0.29 (48227) hydrogen bonds : bond 0.04024 / 2.68 ( 1576) hydrogen bonds : angle 4.17572 / 2.99 ( 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 189 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.351 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: -0.2442 (ttt) cc_final: -0.2730 (ttt) REVERT: A 219 MET cc_start: 0.9377 (OUTLIER) cc_final: 0.8998 (mpp) REVERT: A 332 MET cc_start: 0.8980 (mmm) cc_final: 0.8256 (tmm) REVERT: A 740 MET cc_start: 0.8449 (tmm) cc_final: 0.8227 (tmm) REVERT: A 757 MET cc_start: 0.9445 (tmm) cc_final: 0.9089 (tmm) REVERT: B 46 MET cc_start: 0.2255 (pmm) cc_final: 0.1788 (pmm) REVERT: B 475 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8658 (p) REVERT: C 84 MET cc_start: 0.8972 (ttp) cc_final: 0.8393 (tmm) REVERT: C 110 TYR cc_start: 0.8122 (m-10) cc_final: 0.7859 (m-80) REVERT: C 275 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: C 475 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8631 (t) REVERT: C 757 MET cc_start: 0.9425 (ttp) cc_final: 0.8858 (tmm) REVERT: D 64 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8215 (mtm-85) REVERT: D 84 MET cc_start: 0.9048 (ptm) cc_final: 0.8777 (tmm) REVERT: D 134 TYR cc_start: 0.8233 (m-80) cc_final: 0.7875 (m-80) REVERT: D 219 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8759 (mpp) REVERT: D 757 MET cc_start: 0.9389 (ttm) cc_final: 0.8805 (tmm) REVERT: F 344 MET cc_start: 0.8686 (pmm) cc_final: 0.8446 (pmm) REVERT: F 427 MET cc_start: 0.9218 (mmm) cc_final: 0.9005 (tpt) outliers start: 41 outliers final: 15 residues processed: 177 average time/residue: 0.7742 time to fit residues: 161.8708 Evaluate side-chains 160 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 71 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain F residue 375 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 178 optimal weight: 3.9990 chunk 286 optimal weight: 0.0980 chunk 146 optimal weight: 0.8980 chunk 369 optimal weight: 5.9990 chunk 82 optimal weight: 0.0470 chunk 204 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.119493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.068451 restraints weight = 100962.065| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.60 r_work: 0.2727 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 35670 Z= 0.101 Angle : 0.550 11.335 48227 Z= 0.269 Chirality : 0.042 0.214 5431 Planarity : 0.004 0.060 6311 Dihedral : 6.041 134.950 4900 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 0.91 % Allowed : 11.48 % Favored : 87.61 % 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: 1.72 (0.13), residues: 4388 helix: 1.94 (0.12), residues: 1959 sheet: 0.77 (0.20), residues: 689 loop : 0.51 (0.16), residues: 1740 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 0.012 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/Z covalent geometry : bond 0.00223 / 0.10 (35670) covalent geometry : angle 0.55012 / 0.27 (48227) hydrogen bonds : bond 0.03253 / 2.16 ( 1576) hydrogen bonds : angle 3.94982 / 2.83 ( 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 181 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.375 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 84 MET cc_start: -0.2583 (ttt) cc_final: -0.2789 (ttt) REVERT: A 219 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9134 (mpp) REVERT: A 275 MET cc_start: 0.8808 (mmt) cc_final: 0.8596 (mmt) REVERT: A 332 MET cc_start: 0.9024 (mmm) cc_final: 0.8678 (tmm) REVERT: A 737 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: A 757 MET cc_start: 0.9468 (tmm) cc_final: 0.9123 (tmm) REVERT: B 46 MET cc_start: 0.2422 (OUTLIER) cc_final: 0.1902 (pmm) REVERT: B 475 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8624 (p) REVERT: B 508 MET cc_start: 0.8569 (mtp) cc_final: 0.8334 (mtm) REVERT: C 64 ARG cc_start: 0.8917 (mmm-85) cc_final: 0.8145 (mtm110) REVERT: C 84 MET cc_start: 0.9030 (ttp) cc_final: 0.8393 (tmm) REVERT: C 110 TYR cc_start: 0.8198 (m-10) cc_final: 0.7932 (m-80) REVERT: C 336 LYS cc_start: 0.8775 (tmtt) cc_final: 0.8567 (tptt) REVERT: C 475 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8575 (t) REVERT: C 757 MET cc_start: 0.9382 (ttp) cc_final: 0.8854 (tmm) REVERT: D 46 MET cc_start: 0.8413 (ptt) cc_final: 0.8090 (pmm) REVERT: D 64 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8259 (mtm-85) REVERT: D 84 MET cc_start: 0.9139 (ptm) cc_final: 0.8806 (tmm) REVERT: D 134 TYR cc_start: 0.7957 (m-80) cc_final: 0.7657 (m-80) REVERT: D 757 MET cc_start: 0.9360 (ttm) cc_final: 0.8801 (tmm) REVERT: E 388 MET cc_start: 0.8512 (mtt) cc_final: 0.8170 (mtm) REVERT: F 344 MET cc_start: 0.8698 (pmm) cc_final: 0.8462 (pmm) REVERT: F 427 MET cc_start: 0.9141 (mmm) cc_final: 0.8933 (tpt) outliers start: 34 outliers final: 12 residues processed: 172 average time/residue: 0.8042 time to fit residues: 163.9408 Evaluate side-chains 154 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET 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 46 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 464 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: 1.9990 chunk 333 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 345 optimal weight: 0.0670 chunk 329 optimal weight: 6.9990 chunk 375 optimal weight: 50.0000 chunk 376 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 378 optimal weight: 40.0000 chunk 242 optimal weight: 0.0370 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.118311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.066888 restraints weight = 100776.515| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.59 r_work: 0.2752 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35670 Z= 0.171 Angle : 0.581 11.534 48227 Z= 0.283 Chirality : 0.043 0.240 5431 Planarity : 0.004 0.062 6311 Dihedral : 5.999 133.046 4900 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 0.80 % Allowed : 11.78 % Favored : 87.42 % 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: 1.72 (0.13), residues: 4388 helix: 1.94 (0.12), residues: 1957 sheet: 0.76 (0.20), residues: 692 loop : 0.50 (0.16), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 711 TYR 0.017 0.001 TYR F 143 PHE 0.012 0.001 PHE F 674 TRP 0.009 0.001 TRP D 551 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (35670) covalent geometry : angle 0.58117 / 0.28 (48227) hydrogen bonds : bond 0.03553 / 2.37 ( 1576) hydrogen bonds : angle 4.01528 / 2.87 ( 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 172 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.481 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: -0.2637 (ttt) cc_final: -0.2844 (ttt) REVERT: A 219 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8847 (mpp) REVERT: A 275 MET cc_start: 0.8851 (mmt) cc_final: 0.8570 (mmt) REVERT: A 332 MET cc_start: 0.8976 (mmm) cc_final: 0.8266 (tmm) REVERT: A 757 MET cc_start: 0.9456 (tmm) cc_final: 0.9092 (tmm) REVERT: B 46 MET cc_start: 0.2395 (OUTLIER) cc_final: 0.1923 (pmm) REVERT: B 427 MET cc_start: 0.8817 (ppp) cc_final: 0.8379 (ppp) REVERT: B 475 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 740 MET cc_start: 0.8884 (tpp) cc_final: 0.8214 (tmm) REVERT: C 84 MET cc_start: 0.8877 (ttp) cc_final: 0.8368 (tmm) REVERT: C 110 TYR cc_start: 0.8230 (m-10) cc_final: 0.7952 (m-80) REVERT: C 475 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8597 (t) REVERT: C 740 MET cc_start: 0.9529 (mmm) cc_final: 0.9222 (tmm) REVERT: C 757 MET cc_start: 0.9372 (ttp) cc_final: 0.8865 (tmm) REVERT: D 64 ARG cc_start: 0.8779 (mtp85) cc_final: 0.8297 (mtm-85) REVERT: D 84 MET cc_start: 0.9172 (ptm) cc_final: 0.8789 (tmm) REVERT: D 134 TYR cc_start: 0.8220 (m-80) cc_final: 0.7936 (m-80) REVERT: D 561 GLU cc_start: 0.8939 (tt0) cc_final: 0.8460 (tp30) REVERT: D 757 MET cc_start: 0.9355 (ttm) cc_final: 0.8806 (tmm) REVERT: F 344 MET cc_start: 0.8718 (pmm) cc_final: 0.8481 (pmm) outliers start: 30 outliers final: 15 residues processed: 163 average time/residue: 0.8302 time to fit residues: 159.6081 Evaluate side-chains 156 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET 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 611 MET Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 283 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 71 VAL Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 464 LEU 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: 0.9980 chunk 251 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 426 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 360 optimal weight: 0.0870 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.118669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.067485 restraints weight = 100550.411| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.59 r_work: 0.2769 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3094 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= 0.134 Angle : 0.573 12.456 48227 Z= 0.278 Chirality : 0.043 0.250 5431 Planarity : 0.004 0.069 6311 Dihedral : 5.929 128.648 4900 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.72 % Allowed : 12.15 % Favored : 87.13 % 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: 1.75 (0.13), residues: 4388 helix: 1.97 (0.12), residues: 1943 sheet: 0.78 (0.20), residues: 690 loop : 0.51 (0.16), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 711 TYR 0.017 0.001 TYR F 143 PHE 0.012 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/Z covalent geometry : bond 0.00316 / 0.13 (35670) covalent geometry : angle 0.57280 / 0.28 (48227) hydrogen bonds : bond 0.03369 / 2.25 ( 1576) hydrogen bonds : angle 3.95734 / 2.83 ( 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 165 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.296 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: 0.9383 (OUTLIER) cc_final: 0.8840 (mpp) REVERT: A 275 MET cc_start: 0.8865 (mmt) cc_final: 0.8565 (mmt) REVERT: A 332 MET cc_start: 0.8984 (mmm) cc_final: 0.8293 (tmm) REVERT: A 449 MET cc_start: 0.8594 (tmm) cc_final: 0.7990 (tpp) REVERT: A 737 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: A 757 MET cc_start: 0.9450 (tmm) cc_final: 0.9091 (tmm) REVERT: B 46 MET cc_start: 0.2389 (OUTLIER) cc_final: 0.1925 (pmm) REVERT: B 475 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8659 (p) REVERT: C 84 MET cc_start: 0.8893 (ttp) cc_final: 0.8455 (tmm) REVERT: C 110 TYR cc_start: 0.8226 (m-10) cc_final: 0.7928 (m-80) REVERT: C 475 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 740 MET cc_start: 0.9528 (mmm) cc_final: 0.9062 (tmm) REVERT: C 757 MET cc_start: 0.9370 (ttp) cc_final: 0.8875 (tmm) REVERT: D 46 MET cc_start: 0.8484 (ptt) cc_final: 0.8122 (pmm) REVERT: D 64 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8321 (mtm-85) REVERT: D 84 MET cc_start: 0.9176 (ptm) cc_final: 0.8802 (tmm) REVERT: D 134 TYR cc_start: 0.8202 (m-80) cc_final: 0.7906 (m-80) REVERT: D 561 GLU cc_start: 0.8965 (tt0) cc_final: 0.8467 (tp30) REVERT: D 757 MET cc_start: 0.9338 (ttm) cc_final: 0.8782 (tmm) REVERT: F 344 MET cc_start: 0.8718 (pmm) cc_final: 0.8474 (pmm) REVERT: F 427 MET cc_start: 0.9188 (mmm) cc_final: 0.8965 (tpt) outliers start: 27 outliers final: 18 residues processed: 158 average time/residue: 0.7563 time to fit residues: 141.6009 Evaluate side-chains 161 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 252 THR 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 46 MET 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 611 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 407 VAL 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: 0.3980 chunk 64 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 418 optimal weight: 10.0000 chunk 284 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 295 optimal weight: 0.0170 chunk 289 optimal weight: 0.8980 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.118858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067668 restraints weight = 100557.732| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.61 r_work: 0.2705 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3138 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= 0.123 Angle : 0.576 13.439 48227 Z= 0.278 Chirality : 0.043 0.269 5431 Planarity : 0.004 0.073 6311 Dihedral : 5.882 125.798 4900 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.60 % Favored : 97.33 % Rotamer: Outliers : 0.80 % Allowed : 12.29 % Favored : 86.91 % 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: 1.79 (0.13), residues: 4388 helix: 2.00 (0.12), residues: 1941 sheet: 0.83 (0.20), residues: 679 loop : 0.54 (0.16), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 711 TYR 0.017 0.001 TYR F 143 PHE 0.013 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/Z covalent geometry : bond 0.00287 / 0.12 (35670) covalent geometry : angle 0.57633 / 0.28 (48227) hydrogen bonds : bond 0.03292 / 2.20 ( 1576) hydrogen bonds : angle 3.93996 / 2.82 ( 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 169 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.308 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: 0.9405 (OUTLIER) cc_final: 0.9181 (mpp) REVERT: A 275 MET cc_start: 0.8804 (mmt) cc_final: 0.8596 (mmt) REVERT: A 332 MET cc_start: 0.8975 (mmm) cc_final: 0.8619 (tmm) REVERT: A 449 MET cc_start: 0.8583 (tmm) cc_final: 0.7992 (tpp) REVERT: A 550 MET cc_start: 0.8894 (ptm) cc_final: 0.8541 (ttp) REVERT: A 757 MET cc_start: 0.9445 (tmm) cc_final: 0.9087 (tmm) REVERT: B 46 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.1865 (pmm) REVERT: B 475 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8609 (p) REVERT: B 740 MET cc_start: 0.8804 (tpp) cc_final: 0.8079 (tmm) REVERT: C 64 ARG cc_start: 0.8837 (mmm-85) cc_final: 0.8123 (mtm110) REVERT: C 84 MET cc_start: 0.8997 (ttp) cc_final: 0.8504 (tmm) REVERT: C 110 TYR cc_start: 0.8247 (m-10) cc_final: 0.7947 (m-80) REVERT: C 475 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8539 (t) REVERT: C 740 MET cc_start: 0.9500 (mmm) cc_final: 0.8869 (tmm) REVERT: C 757 MET cc_start: 0.9397 (ttp) cc_final: 0.8891 (tmm) REVERT: D 46 MET cc_start: 0.8495 (ptt) cc_final: 0.8129 (pmm) REVERT: D 64 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8327 (mtm-85) REVERT: D 84 MET cc_start: 0.9151 (ptm) cc_final: 0.8763 (tmm) REVERT: D 134 TYR cc_start: 0.8198 (m-80) cc_final: 0.7919 (m-80) REVERT: D 561 GLU cc_start: 0.8995 (tt0) cc_final: 0.8455 (tp30) REVERT: D 757 MET cc_start: 0.9335 (ttm) cc_final: 0.8798 (tmm) REVERT: F 344 MET cc_start: 0.8691 (pmm) cc_final: 0.8456 (pmm) REVERT: F 427 MET cc_start: 0.9168 (mmm) cc_final: 0.8952 (tpt) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 0.7868 time to fit residues: 149.3917 Evaluate side-chains 160 residues out of total 3791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 252 THR 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 495 TYR 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 46 MET 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 D residue 71 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 388 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 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: 5.9990 chunk 144 optimal weight: 0.9990 chunk 350 optimal weight: 0.0370 chunk 322 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 431 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 387 optimal weight: 40.0000 chunk 403 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 406 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.119399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068583 restraints weight = 100533.570| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.58 r_work: 0.2726 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 35670 Z= 0.101 Angle : 0.565 13.246 48227 Z= 0.273 Chirality : 0.042 0.263 5431 Planarity : 0.004 0.059 6311 Dihedral : 5.760 121.507 4900 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 0.70 % Allowed : 12.39 % Favored : 86.91 % 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: 1.84 (0.13), residues: 4388 helix: 2.04 (0.12), residues: 1936 sheet: 0.83 (0.20), residues: 686 loop : 0.59 (0.16), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG C 711 TYR 0.017 0.001 TYR F 143 PHE 0.013 0.001 PHE F 674 TRP 0.007 0.001 TRP D 551 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (35670) covalent geometry : angle 0.56475 / 0.27 (48227) hydrogen bonds : bond 0.03089 / 2.07 ( 1576) hydrogen bonds : angle 3.88291 / 2.78 ( 4569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13031.24 seconds wall clock time: 222 minutes 28.90 seconds (13348.90 seconds total)