Starting phenix.real_space_refine on Fri Mar 6 22:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln2_23446/03_2026/7ln2_23446.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 7 5.21 5 S 178 5.16 5 C 21879 2.51 5 N 6200 2.21 5 O 6646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34941 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5720 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 691} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 5803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5803 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 5866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5866 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 37, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 5865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5865 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 710} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 5712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5712 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 4, 'PTRANS': 35, 'TRANS': 692} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 5506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5506 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 659} 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.18, per 1000 atoms: 0.26 Number of scatterers: 34941 At special positions: 0 Unit cell: (155.434, 172.704, 131.687, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 178 16.00 P 31 15.00 Mg 7 11.99 O 6646 8.00 N 6200 7.00 C 21879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8288 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 33 sheets defined 52.8% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.502A pdb=" N VAL A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 190 through 200 removed outlier: 3.632A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.589A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.941A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.552A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.257A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.509A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.014A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.502A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 4.726A pdb=" N THR A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 583 removed outlier: 4.049A 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 671 through 679 Processing helix chain 'A' and resid 683 through 714 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.650A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.926A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.201A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 removed outlier: 4.052A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.917A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 388 removed outlier: 4.554A pdb=" N ASN B 387 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET B 388 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.579A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 462 through 466 removed outlier: 4.249A pdb=" N GLU B 466 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.697A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 4.358A pdb=" N GLN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.504A pdb=" N GLU B 546 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 547 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 579 through 582 Processing helix chain 'B' and resid 595 through 609 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.632A pdb=" N LEU B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.644A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.617A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 removed outlier: 3.695A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 removed outlier: 3.616A pdb=" N ILE C 16 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.827A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 190 through 199 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.230A 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: 4.146A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 271 through 275 removed outlier: 4.437A pdb=" N MET C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 275' Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.533A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.875A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.545A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 408 through 430 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 462 through 466 removed outlier: 4.440A pdb=" N GLU C 466 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.778A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.587A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 4.114A pdb=" N LEU C 547 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 714 Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.563A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 removed outlier: 3.510A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 18 removed outlier: 3.787A pdb=" N ILE D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.853A pdb=" N GLU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.085A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 4.295A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.710A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.209A 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 373 through 386 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.689A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.640A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.067A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 544 through 548 removed outlier: 4.396A pdb=" N LEU D 547 " --> pdb=" O GLY D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.564A pdb=" N ALA D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.994A pdb=" N ILE D 582 " --> pdb=" O GLN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 609 removed outlier: 4.318A pdb=" N GLY D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP D 598 " --> pdb=" O GLY D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 635 removed outlier: 3.806A pdb=" N LEU D 634 " --> pdb=" O ASP D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.905A 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 743 removed outlier: 3.552A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 removed outlier: 3.594A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 92 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 139 Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.070A 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: 3.594A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 271 through 275 removed outlier: 4.290A 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 Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.130A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 338 removed outlier: 3.519A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.606A pdb=" N ARG E 358 " --> pdb=" O ASP E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.916A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 427 Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.641A pdb=" N GLU E 466 " --> pdb=" O ALA E 463 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 468 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.123A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 544 through 548 removed outlier: 3.633A pdb=" N LEU E 547 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 569 removed outlier: 3.721A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 592 Processing helix chain 'E' and resid 595 through 611 removed outlier: 3.775A pdb=" N ARG E 599 " --> pdb=" O GLY E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.885A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.637A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 Processing helix chain 'E' and resid 732 through 743 removed outlier: 3.787A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.518A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.937A pdb=" N TYR F 138 " --> pdb=" O TYR F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.931A pdb=" N GLU F 194 " --> pdb=" O LYS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.513A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 296 Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 318 through 335 removed outlier: 3.955A pdb=" N LEU F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.526A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 388 removed outlier: 3.753A pdb=" N ASN F 387 " --> pdb=" O ILE F 383 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET F 388 " --> pdb=" O HIS F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.134A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.651A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.699A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 559 through 570 Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.605A pdb=" N ILE F 582 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 614 removed outlier: 3.648A pdb=" N THR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 614 " --> pdb=" O GLY F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.532A pdb=" N ILE F 628 " --> pdb=" O ARG F 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 removed outlier: 3.965A 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: 3.826A 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 29 removed outlier: 7.453A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 40 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 3.886A pdb=" N ASP A 150 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.838A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.449A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 5.762A 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: 6.579A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 118 removed outlier: 7.728A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 150 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AB1, first strand: chain 'B' and resid 265 through 270 removed outlier: 5.738A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.464A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.679A pdb=" N SER C 40 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 41 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP C 55 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 115 through 118 removed outlier: 6.447A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB6, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.223A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.604A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.552A pdb=" N LYS D 60 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 151 through 154 removed outlier: 7.106A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.864A pdb=" N ILE D 146 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.304A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.546A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 66 through 70 removed outlier: 7.674A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 151 through 154 removed outlier: 3.594A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.075A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.397A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 30 removed outlier: 5.881A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 39 through 41 removed outlier: 3.881A pdb=" N ASP F 55 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 113 through 115 Processing sheet with id=AD3, first strand: chain 'F' and resid 117 through 118 removed outlier: 3.714A pdb=" N ASP F 150 " --> pdb=" O VAL F 165 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD5, first strand: chain 'F' and resid 266 through 270 removed outlier: 6.618A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.588A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1605 hydrogen bonds defined for protein. 4644 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: 8.19 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11899 1.34 - 1.46: 4859 1.46 - 1.58: 18448 1.58 - 1.70: 34 1.70 - 1.82: 284 Bond restraints: 35524 Sorted by residual: bond pdb=" CB PRO F 519 " pdb=" CG PRO F 519 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.12e+00 bond pdb=" CB PRO A 472 " pdb=" CG PRO A 472 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 bond pdb=" N PHE B 768 " pdb=" CA PHE B 768 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.29e+00 bond pdb=" CA THR B 448 " pdb=" CB THR B 448 " ideal model delta sigma weight residual 1.534 1.560 -0.025 1.77e-02 3.19e+03 2.07e+00 bond pdb=" CB ILE B 582 " pdb=" CG2 ILE B 582 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 ... (remaining 35519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 47498 2.56 - 5.11: 480 5.11 - 7.67: 50 7.67 - 10.22: 5 10.22 - 12.78: 1 Bond angle restraints: 48034 Sorted by residual: angle pdb=" CA PRO F 519 " pdb=" N PRO F 519 " pdb=" CD PRO F 519 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" N PRO F 519 " pdb=" CD PRO F 519 " pdb=" CG PRO F 519 " ideal model delta sigma weight residual 103.20 97.74 5.46 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C ASP C 431 " pdb=" N LEU C 432 " pdb=" CA LEU C 432 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA ALA D 297 " pdb=" C ALA D 297 " pdb=" N PRO D 298 " ideal model delta sigma weight residual 118.44 123.96 -5.52 1.59e+00 3.96e-01 1.21e+01 angle pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N PRO A 298 " ideal model delta sigma weight residual 118.44 123.94 -5.50 1.59e+00 3.96e-01 1.20e+01 ... (remaining 48029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 21330 29.31 - 58.61: 725 58.61 - 87.92: 84 87.92 - 117.23: 9 117.23 - 146.53: 5 Dihedral angle restraints: 22153 sinusoidal: 9384 harmonic: 12769 Sorted by residual: dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 86.53 -146.53 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PB ADP B 902 " pdb=" PA ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 77.28 -137.28 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O2A ADP B 902 " pdb=" O3A ADP B 902 " pdb=" PA ADP B 902 " pdb=" PB ADP B 902 " ideal model delta sinusoidal sigma weight residual -60.00 72.33 -132.32 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 22150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3579 0.035 - 0.069: 1168 0.069 - 0.104: 454 0.104 - 0.139: 190 0.139 - 0.173: 9 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CB ILE F 82 " pdb=" CA ILE F 82 " pdb=" CG1 ILE F 82 " pdb=" CG2 ILE F 82 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA ILE F 151 " pdb=" N ILE F 151 " pdb=" C ILE F 151 " pdb=" CB ILE F 151 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 5397 not shown) Planarity restraints: 6291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 518 " -0.067 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO F 519 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO F 519 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 519 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 773 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.24e+00 pdb=" N PRO C 774 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 774 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 774 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO C 545 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.035 5.00e-02 4.00e+02 ... (remaining 6288 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 248 2.57 - 3.15: 28614 3.15 - 3.73: 55657 3.73 - 4.32: 75825 4.32 - 4.90: 123876 Nonbonded interactions: 284220 Sorted by model distance: nonbonded pdb=" O1G ATP C 901 " pdb="MG MG C 903 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR D 252 " pdb="MG MG D 903 " model vdw 1.989 2.170 nonbonded pdb=" O2B ATP C 901 " pdb="MG MG C 903 " model vdw 1.994 2.170 nonbonded pdb=" O1G ATP E 902 " pdb="MG MG E 904 " model vdw 2.000 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 903 " model vdw 2.043 2.170 ... (remaining 284215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )) or resid 53 \ 5 through 545 or resid 558 through 583 or resid 596 through 762)) selection = (chain 'B' and (resid 23 through 461 or resid 472 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 545 or \ resid 558 through 583 or resid 596 through 762)) selection = (chain 'C' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'D' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'E' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 461 or resid 472 through 507 or \ (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 9 through 533 or (resid 534 and (name N or name CA or name C or name O or name C \ B )) or resid 535 through 545 or resid 558 through 583 or resid 596 through 762) \ ) selection = (chain 'F' and (resid 23 through 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 507 or (resid 508 and (name N o \ r name CA or name C or name O or name CB )) or resid 509 through 533 or (resid 5 \ 34 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.250 Find NCS groups from input model: 1.090 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:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 35524 Z= 0.172 Angle : 0.650 12.781 48034 Z= 0.346 Chirality : 0.043 0.173 5400 Planarity : 0.005 0.094 6291 Dihedral : 14.331 146.534 13865 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.12), residues: 4377 helix: 1.50 (0.12), residues: 1955 sheet: 1.14 (0.19), residues: 639 loop : 0.51 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 638 TYR 0.020 0.002 TYR D 244 PHE 0.023 0.002 PHE F 290 TRP 0.026 0.002 TRP A 454 HIS 0.009 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00396 (35524) covalent geometry : angle 0.65035 (48034) hydrogen bonds : bond 0.17779 ( 1605) hydrogen bonds : angle 6.29493 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 MET cc_start: -0.0702 (tmm) cc_final: -0.1430 (ptm) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2443 time to fit residues: 96.0754 Evaluate side-chains 146 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.0570 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN B 533 ASN B 624 ASN C 660 ASN D 19 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN F 421 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.076644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050333 restraints weight = 226873.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051094 restraints weight = 135301.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.050782 restraints weight = 88631.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050873 restraints weight = 82348.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050938 restraints weight = 81504.838| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35524 Z= 0.220 Angle : 0.658 9.791 48034 Z= 0.333 Chirality : 0.044 0.199 5400 Planarity : 0.005 0.069 6291 Dihedral : 10.112 137.191 5110 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.33 % Rotamer: Outliers : 0.46 % Allowed : 5.49 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.13), residues: 4377 helix: 1.77 (0.11), residues: 1988 sheet: 0.89 (0.19), residues: 672 loop : 0.63 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 708 TYR 0.017 0.002 TYR A 110 PHE 0.022 0.002 PHE A 742 TRP 0.016 0.002 TRP A 454 HIS 0.009 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00473 (35524) covalent geometry : angle 0.65751 (48034) hydrogen bonds : bond 0.04293 ( 1605) hydrogen bonds : angle 5.06815 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.408 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: A 344 MET cc_start: 0.9365 (pmm) cc_final: 0.9002 (pmm) REVERT: B 344 MET cc_start: 0.8171 (mpp) cc_final: 0.7894 (mpp) REVERT: B 550 MET cc_start: 0.9079 (ppp) cc_final: 0.8439 (ppp) REVERT: C 427 MET cc_start: 0.8241 (tpt) cc_final: 0.7801 (tpp) REVERT: D 46 MET cc_start: 0.5332 (mpp) cc_final: 0.5124 (ptp) REVERT: D 388 MET cc_start: 0.8275 (ptp) cc_final: 0.7991 (ptp) REVERT: D 757 MET cc_start: 0.9160 (tmm) cc_final: 0.8958 (tmm) REVERT: E 608 MET cc_start: 0.9388 (ptm) cc_final: 0.9178 (ptm) REVERT: E 678 MET cc_start: 0.9106 (mmm) cc_final: 0.8870 (mmm) REVERT: F 219 MET cc_start: 0.8645 (mmp) cc_final: 0.8422 (mmt) REVERT: F 332 MET cc_start: 0.8543 (tpp) cc_final: 0.8335 (tpp) REVERT: F 449 MET cc_start: 0.8947 (tpp) cc_final: 0.8746 (tpp) outliers start: 17 outliers final: 11 residues processed: 165 average time/residue: 0.2170 time to fit residues: 61.0950 Evaluate side-chains 148 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 737 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 277 optimal weight: 3.9990 chunk 301 optimal weight: 40.0000 chunk 172 optimal weight: 0.6980 chunk 169 optimal weight: 8.9990 chunk 278 optimal weight: 0.9980 chunk 3 optimal weight: 40.0000 chunk 364 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 326 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.077028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047046 restraints weight = 226250.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046297 restraints weight = 128196.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046770 restraints weight = 91948.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046954 restraints weight = 76014.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047172 restraints weight = 69728.735| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35524 Z= 0.164 Angle : 0.575 9.669 48034 Z= 0.289 Chirality : 0.042 0.188 5400 Planarity : 0.004 0.054 6291 Dihedral : 9.791 128.861 5110 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer: Outliers : 0.73 % Allowed : 6.94 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 4377 helix: 1.94 (0.12), residues: 1988 sheet: 0.83 (0.19), residues: 660 loop : 0.67 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.012 0.001 TYR F 495 PHE 0.013 0.001 PHE A 742 TRP 0.014 0.001 TRP F 476 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00358 (35524) covalent geometry : angle 0.57539 (48034) hydrogen bonds : bond 0.03914 ( 1605) hydrogen bonds : angle 4.72926 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.346 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 344 MET cc_start: 0.9248 (pmm) cc_final: 0.8859 (pmm) REVERT: B 344 MET cc_start: 0.8169 (mpp) cc_final: 0.7878 (mpp) REVERT: B 442 MET cc_start: 0.8917 (mmm) cc_final: 0.8083 (mmm) REVERT: C 427 MET cc_start: 0.8046 (tpt) cc_final: 0.7750 (tpp) REVERT: D 45 LYS cc_start: 0.8573 (tptt) cc_final: 0.8325 (tppt) REVERT: D 46 MET cc_start: 0.5206 (mpp) cc_final: 0.4971 (ptp) REVERT: D 332 MET cc_start: 0.8995 (mtp) cc_final: 0.8562 (ttm) REVERT: D 757 MET cc_start: 0.9045 (tmm) cc_final: 0.8800 (tmm) REVERT: E 678 MET cc_start: 0.9079 (mmm) cc_final: 0.8859 (mmm) REVERT: F 332 MET cc_start: 0.8488 (tpp) cc_final: 0.8262 (tpp) REVERT: F 611 MET cc_start: 0.8155 (mmm) cc_final: 0.7951 (mmm) REVERT: F 678 MET cc_start: 0.9349 (mtp) cc_final: 0.9146 (mtp) outliers start: 27 outliers final: 10 residues processed: 159 average time/residue: 0.2014 time to fit residues: 55.7178 Evaluate side-chains 140 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 363 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 223 optimal weight: 30.0000 chunk 179 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 254 optimal weight: 0.4980 chunk 358 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 624 ASN B 641 GLN C 19 GLN C 458 GLN C 533 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.084776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.057140 restraints weight = 135078.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.057476 restraints weight = 113073.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057241 restraints weight = 100019.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.057410 restraints weight = 90513.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057417 restraints weight = 89710.340| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.005 0.061 35524 Z= 0.240 Angle : 0.638 12.036 48034 Z= 0.319 Chirality : 0.043 0.185 5400 Planarity : 0.005 0.059 6291 Dihedral : 9.659 121.389 5110 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Rotamer: Outliers : 0.99 % Allowed : 8.79 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 4377 helix: 1.77 (0.12), residues: 2009 sheet: 0.77 (0.19), residues: 647 loop : 0.56 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 638 TYR 0.016 0.001 TYR D 134 PHE 0.016 0.002 PHE F 674 TRP 0.009 0.002 TRP F 476 HIS 0.006 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00513 (35524) covalent geometry : angle 0.63849 (48034) hydrogen bonds : bond 0.03837 ( 1605) hydrogen bonds : angle 4.79195 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8991 (pmm) cc_final: 0.8546 (pmm) REVERT: B 344 MET cc_start: 0.8154 (mpp) cc_final: 0.7881 (mpp) REVERT: B 421 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: B 442 MET cc_start: 0.8814 (mmm) cc_final: 0.8096 (mmm) REVERT: B 740 MET cc_start: 0.8725 (ppp) cc_final: 0.8520 (ppp) REVERT: C 46 MET cc_start: 0.6995 (mtt) cc_final: 0.6692 (ptp) REVERT: C 427 MET cc_start: 0.8353 (tpt) cc_final: 0.7825 (tpp) REVERT: D 332 MET cc_start: 0.8926 (mtp) cc_final: 0.8474 (ttm) REVERT: D 757 MET cc_start: 0.9175 (tmm) cc_final: 0.8909 (tmm) REVERT: E 173 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: E 335 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8927 (tp) REVERT: E 449 MET cc_start: 0.8965 (mmm) cc_final: 0.8741 (mmm) REVERT: E 678 MET cc_start: 0.9164 (mmm) cc_final: 0.8896 (mmm) REVERT: F 332 MET cc_start: 0.8573 (tpp) cc_final: 0.8325 (tpp) outliers start: 37 outliers final: 15 residues processed: 153 average time/residue: 0.1995 time to fit residues: 53.6226 Evaluate side-chains 143 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 668 LYS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 58 optimal weight: 8.9990 chunk 375 optimal weight: 40.0000 chunk 45 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 2 optimal weight: 40.0000 chunk 251 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.086279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.056390 restraints weight = 124693.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056919 restraints weight = 101447.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057226 restraints weight = 90335.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057346 restraints weight = 84316.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057478 restraints weight = 81747.009| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 35524 Z= 0.260 Angle : 0.639 9.923 48034 Z= 0.321 Chirality : 0.043 0.197 5400 Planarity : 0.004 0.055 6291 Dihedral : 9.432 117.415 5110 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.17 % Favored : 97.76 % Rotamer: Outliers : 0.91 % Allowed : 9.98 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.59 (0.13), residues: 4377 helix: 1.73 (0.11), residues: 2009 sheet: 0.70 (0.19), residues: 648 loop : 0.53 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 338 TYR 0.015 0.001 TYR A 495 PHE 0.018 0.002 PHE F 674 TRP 0.009 0.001 TRP F 476 HIS 0.006 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00554 (35524) covalent geometry : angle 0.63868 (48034) hydrogen bonds : bond 0.03772 ( 1605) hydrogen bonds : angle 4.79440 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9024 (pmm) cc_final: 0.8588 (pmm) REVERT: B 344 MET cc_start: 0.8186 (mpp) cc_final: 0.7881 (mpp) REVERT: B 421 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8787 (tm-30) REVERT: B 442 MET cc_start: 0.8834 (mmm) cc_final: 0.7965 (mmm) REVERT: B 638 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8483 (ptp90) REVERT: C 332 MET cc_start: 0.8459 (mmm) cc_final: 0.8204 (mmm) REVERT: C 427 MET cc_start: 0.8229 (tpt) cc_final: 0.7745 (tpp) REVERT: D 332 MET cc_start: 0.9002 (mtp) cc_final: 0.8523 (ttm) REVERT: D 757 MET cc_start: 0.9160 (tmm) cc_final: 0.8885 (tmm) REVERT: E 173 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6673 (m-80) REVERT: E 335 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8950 (tp) REVERT: E 427 MET cc_start: 0.9129 (ttp) cc_final: 0.8518 (tpt) REVERT: E 678 MET cc_start: 0.9135 (mmm) cc_final: 0.8860 (mmm) REVERT: E 757 MET cc_start: 0.9416 (mtp) cc_final: 0.9209 (ptp) REVERT: F 332 MET cc_start: 0.8625 (tpp) cc_final: 0.8342 (tpp) REVERT: F 449 MET cc_start: 0.8866 (tpt) cc_final: 0.8616 (tpt) outliers start: 34 outliers final: 17 residues processed: 151 average time/residue: 0.2081 time to fit residues: 54.8536 Evaluate side-chains 146 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 231 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 421 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.089948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.059432 restraints weight = 102181.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.059550 restraints weight = 97085.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059615 restraints weight = 94511.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059615 restraints weight = 92911.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.059615 restraints weight = 92911.909| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35524 Z= 0.103 Angle : 0.556 10.168 48034 Z= 0.275 Chirality : 0.042 0.185 5400 Planarity : 0.004 0.053 6291 Dihedral : 8.938 113.846 5110 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 0.86 % Allowed : 10.46 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.90 (0.13), residues: 4377 helix: 2.05 (0.12), residues: 1986 sheet: 0.83 (0.20), residues: 626 loop : 0.64 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.016 0.001 TYR D 134 PHE 0.015 0.001 PHE F 674 TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00224 (35524) covalent geometry : angle 0.55595 (48034) hydrogen bonds : bond 0.03358 ( 1605) hydrogen bonds : angle 4.39461 ( 4644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.9200 (tp) cc_final: 0.8964 (mt) REVERT: A 344 MET cc_start: 0.9247 (pmm) cc_final: 0.8730 (pmm) REVERT: A 611 MET cc_start: 0.7297 (mmt) cc_final: 0.6654 (mmm) REVERT: B 344 MET cc_start: 0.8277 (mpp) cc_final: 0.7957 (mpp) REVERT: B 421 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8800 (tm-30) REVERT: B 442 MET cc_start: 0.8989 (mmm) cc_final: 0.7999 (mmm) REVERT: C 46 MET cc_start: 0.6999 (mtt) cc_final: 0.6578 (ptp) REVERT: C 427 MET cc_start: 0.8169 (tpt) cc_final: 0.7780 (tpp) REVERT: D 46 MET cc_start: 0.5523 (ptp) cc_final: 0.5201 (ptp) REVERT: D 757 MET cc_start: 0.9155 (tmm) cc_final: 0.8845 (tmm) REVERT: E 335 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9053 (tp) REVERT: E 427 MET cc_start: 0.8663 (ttp) cc_final: 0.8318 (tpt) REVERT: E 678 MET cc_start: 0.9163 (mmm) cc_final: 0.8927 (mmm) REVERT: F 215 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9022 (mt0) REVERT: F 332 MET cc_start: 0.8610 (tpp) cc_final: 0.8386 (tpp) REVERT: F 344 MET cc_start: 0.9508 (ptp) cc_final: 0.9282 (pmm) REVERT: F 449 MET cc_start: 0.8843 (tpt) cc_final: 0.8584 (tpt) outliers start: 32 outliers final: 14 residues processed: 157 average time/residue: 0.1999 time to fit residues: 55.3035 Evaluate side-chains 144 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 92 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 308 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 387 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.088059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057715 restraints weight = 107754.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057875 restraints weight = 101155.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058031 restraints weight = 97619.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058073 restraints weight = 95595.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058073 restraints weight = 94441.658| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 35524 Z= 0.183 Angle : 0.596 10.804 48034 Z= 0.294 Chirality : 0.042 0.185 5400 Planarity : 0.004 0.054 6291 Dihedral : 8.828 110.899 5110 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 0.83 % Allowed : 11.21 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.88 (0.13), residues: 4377 helix: 2.03 (0.12), residues: 2008 sheet: 0.85 (0.20), residues: 626 loop : 0.60 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 424 TYR 0.014 0.001 TYR D 134 PHE 0.013 0.001 PHE C 230 TRP 0.008 0.001 TRP A 454 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00397 (35524) covalent geometry : angle 0.59614 (48034) hydrogen bonds : bond 0.03411 ( 1605) hydrogen bonds : angle 4.48904 ( 4644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.9228 (tp) cc_final: 0.8957 (mt) REVERT: A 344 MET cc_start: 0.9174 (pmm) cc_final: 0.8697 (pmm) REVERT: A 611 MET cc_start: 0.7413 (mmt) cc_final: 0.6695 (mmm) REVERT: B 344 MET cc_start: 0.8255 (mpp) cc_final: 0.7940 (mpp) REVERT: B 421 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8859 (tm-30) REVERT: B 442 MET cc_start: 0.9000 (mmm) cc_final: 0.8023 (mmm) REVERT: C 332 MET cc_start: 0.8701 (mmm) cc_final: 0.8474 (mmm) REVERT: C 427 MET cc_start: 0.8097 (tpt) cc_final: 0.7655 (tpp) REVERT: D 46 MET cc_start: 0.5654 (ptp) cc_final: 0.5365 (ptp) REVERT: D 757 MET cc_start: 0.9126 (tmm) cc_final: 0.8822 (tmm) REVERT: E 173 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: E 335 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9072 (tp) REVERT: E 427 MET cc_start: 0.8703 (ttp) cc_final: 0.8399 (tpt) REVERT: E 678 MET cc_start: 0.9197 (mmm) cc_final: 0.8970 (mmm) REVERT: F 215 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8988 (mt0) REVERT: F 332 MET cc_start: 0.8620 (tpp) cc_final: 0.8397 (tpp) REVERT: F 449 MET cc_start: 0.8902 (tpt) cc_final: 0.8641 (tpt) outliers start: 31 outliers final: 20 residues processed: 149 average time/residue: 0.1957 time to fit residues: 51.9786 Evaluate side-chains 147 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 270 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 360 optimal weight: 2.9990 chunk 430 optimal weight: 0.0470 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.074257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047953 restraints weight = 231398.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.048820 restraints weight = 143475.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048455 restraints weight = 91232.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.048341 restraints weight = 101541.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.048504 restraints weight = 85929.489| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35524 Z= 0.138 Angle : 0.578 12.588 48034 Z= 0.285 Chirality : 0.042 0.202 5400 Planarity : 0.004 0.057 6291 Dihedral : 8.673 111.244 5110 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.99 % Rotamer: Outliers : 0.91 % Allowed : 11.29 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.94 (0.13), residues: 4377 helix: 2.09 (0.12), residues: 1997 sheet: 0.85 (0.20), residues: 626 loop : 0.64 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 89 TYR 0.014 0.001 TYR D 134 PHE 0.014 0.001 PHE D 52 TRP 0.007 0.001 TRP A 454 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00304 (35524) covalent geometry : angle 0.57816 (48034) hydrogen bonds : bond 0.03299 ( 1605) hydrogen bonds : angle 4.42431 ( 4644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LEU cc_start: 0.9440 (tp) cc_final: 0.9206 (mt) REVERT: A 344 MET cc_start: 0.9160 (pmm) cc_final: 0.8770 (pmm) REVERT: B 344 MET cc_start: 0.8211 (mpp) cc_final: 0.7897 (mpp) REVERT: B 421 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8816 (tm-30) REVERT: B 442 MET cc_start: 0.8769 (mmm) cc_final: 0.8197 (mmm) REVERT: C 46 MET cc_start: 0.7091 (mtt) cc_final: 0.6828 (ptp) REVERT: C 332 MET cc_start: 0.8654 (mmm) cc_final: 0.8381 (mmm) REVERT: C 388 MET cc_start: 0.8652 (mtt) cc_final: 0.8172 (ptp) REVERT: C 427 MET cc_start: 0.8516 (tpt) cc_final: 0.7931 (tpp) REVERT: D 46 MET cc_start: 0.5235 (ptp) cc_final: 0.4688 (ptp) REVERT: D 757 MET cc_start: 0.9252 (tmm) cc_final: 0.8939 (tmm) REVERT: E 84 MET cc_start: 0.3414 (tpt) cc_final: 0.3194 (tpp) REVERT: E 173 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: E 335 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9189 (tp) REVERT: E 427 MET cc_start: 0.9433 (ttp) cc_final: 0.8729 (tpt) REVERT: E 608 MET cc_start: 0.9483 (ptm) cc_final: 0.9265 (ppp) REVERT: E 678 MET cc_start: 0.9178 (mmm) cc_final: 0.8932 (mmm) REVERT: F 332 MET cc_start: 0.8519 (tpp) cc_final: 0.8317 (tpp) outliers start: 34 outliers final: 22 residues processed: 148 average time/residue: 0.1980 time to fit residues: 51.9731 Evaluate side-chains 147 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 0 optimal weight: 70.0000 chunk 328 optimal weight: 7.9990 chunk 410 optimal weight: 30.0000 chunk 402 optimal weight: 20.0000 chunk 367 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 436 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.073134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043981 restraints weight = 233014.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042630 restraints weight = 131682.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043180 restraints weight = 95615.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.043439 restraints weight = 80573.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.043558 restraints weight = 73587.805| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35524 Z= 0.192 Angle : 0.612 12.179 48034 Z= 0.303 Chirality : 0.042 0.204 5400 Planarity : 0.004 0.059 6291 Dihedral : 8.643 110.255 5110 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 11.62 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.13), residues: 4377 helix: 2.01 (0.12), residues: 2011 sheet: 0.75 (0.20), residues: 626 loop : 0.62 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 753 TYR 0.014 0.001 TYR D 134 PHE 0.017 0.001 PHE F 771 TRP 0.010 0.001 TRP A 454 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00415 (35524) covalent geometry : angle 0.61247 (48034) hydrogen bonds : bond 0.03425 ( 1605) hydrogen bonds : angle 4.51559 ( 4644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9133 (pmm) cc_final: 0.8669 (pmm) REVERT: A 449 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8647 (mmm) REVERT: B 344 MET cc_start: 0.8186 (mpp) cc_final: 0.7862 (mpp) REVERT: B 388 MET cc_start: 0.8663 (pmm) cc_final: 0.8272 (pmm) REVERT: B 421 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8845 (tm-30) REVERT: B 442 MET cc_start: 0.8930 (mmm) cc_final: 0.8176 (mmm) REVERT: C 46 MET cc_start: 0.7280 (mtt) cc_final: 0.6999 (ptp) REVERT: C 332 MET cc_start: 0.8501 (mmm) cc_final: 0.8293 (mmm) REVERT: C 388 MET cc_start: 0.8595 (mtt) cc_final: 0.8258 (ptp) REVERT: C 427 MET cc_start: 0.8208 (tpt) cc_final: 0.7643 (tpp) REVERT: D 46 MET cc_start: 0.5466 (ptp) cc_final: 0.4943 (ptp) REVERT: D 757 MET cc_start: 0.9195 (tmm) cc_final: 0.8885 (tmm) REVERT: E 335 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9107 (tp) REVERT: E 427 MET cc_start: 0.9252 (ttp) cc_final: 0.8705 (tpt) REVERT: E 449 MET cc_start: 0.9034 (mmm) cc_final: 0.8812 (mmm) REVERT: E 678 MET cc_start: 0.9174 (mmm) cc_final: 0.8947 (mmm) REVERT: F 344 MET cc_start: 0.9626 (pmm) cc_final: 0.9407 (pmm) REVERT: F 449 MET cc_start: 0.8955 (tpt) cc_final: 0.8740 (tpt) outliers start: 31 outliers final: 21 residues processed: 145 average time/residue: 0.2031 time to fit residues: 52.3749 Evaluate side-chains 147 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 8 optimal weight: 50.0000 chunk 36 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 354 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 307 optimal weight: 40.0000 chunk 39 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.073506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047124 restraints weight = 232797.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.047946 restraints weight = 139481.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047688 restraints weight = 86648.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047708 restraints weight = 89486.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.047821 restraints weight = 78225.153| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35524 Z= 0.167 Angle : 0.606 12.270 48034 Z= 0.301 Chirality : 0.042 0.205 5400 Planarity : 0.004 0.060 6291 Dihedral : 8.542 110.024 5110 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 0.70 % Allowed : 11.94 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % 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: 1.89 (0.13), residues: 4377 helix: 2.03 (0.12), residues: 2009 sheet: 0.74 (0.20), residues: 626 loop : 0.66 (0.16), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 377 TYR 0.013 0.001 TYR D 134 PHE 0.019 0.001 PHE F 771 TRP 0.010 0.001 TRP A 454 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00363 (35524) covalent geometry : angle 0.60640 (48034) hydrogen bonds : bond 0.03373 ( 1605) hydrogen bonds : angle 4.47944 ( 4644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9129 (pmm) cc_final: 0.8735 (pmm) REVERT: A 442 MET cc_start: 0.9250 (tpt) cc_final: 0.8841 (tmm) REVERT: A 449 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8848 (mmm) REVERT: A 611 MET cc_start: 0.7037 (mmt) cc_final: 0.6694 (mmm) REVERT: B 344 MET cc_start: 0.8178 (mpp) cc_final: 0.7828 (mpp) REVERT: B 388 MET cc_start: 0.8601 (pmm) cc_final: 0.8313 (pmm) REVERT: B 421 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8807 (tm-30) REVERT: B 442 MET cc_start: 0.8798 (mmm) cc_final: 0.8181 (mmm) REVERT: C 46 MET cc_start: 0.7266 (mtt) cc_final: 0.6979 (ptp) REVERT: C 332 MET cc_start: 0.8630 (mmm) cc_final: 0.8376 (mmm) REVERT: C 388 MET cc_start: 0.8613 (mtt) cc_final: 0.8253 (ptp) REVERT: C 427 MET cc_start: 0.8457 (tpt) cc_final: 0.7797 (tpp) REVERT: D 46 MET cc_start: 0.5246 (ptp) cc_final: 0.4727 (ptp) REVERT: D 275 MET cc_start: 0.9376 (mmm) cc_final: 0.9083 (mmm) REVERT: D 757 MET cc_start: 0.9235 (tmm) cc_final: 0.8914 (tmm) REVERT: E 335 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9177 (tp) REVERT: E 427 MET cc_start: 0.9403 (ttp) cc_final: 0.8781 (tpt) REVERT: E 608 MET cc_start: 0.9496 (ptm) cc_final: 0.9246 (ppp) REVERT: E 678 MET cc_start: 0.9171 (mmm) cc_final: 0.8930 (mmm) REVERT: E 757 MET cc_start: 0.9501 (ptp) cc_final: 0.9200 (mpp) outliers start: 26 outliers final: 21 residues processed: 143 average time/residue: 0.2013 time to fit residues: 51.2844 Evaluate side-chains 148 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 421 GLN Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 740 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 3 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 382 optimal weight: 40.0000 chunk 399 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.073379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046987 restraints weight = 231338.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.047948 restraints weight = 139912.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047531 restraints weight = 94464.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047582 restraints weight = 84564.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.047572 restraints weight = 78746.446| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35524 Z= 0.148 Angle : 0.602 12.024 48034 Z= 0.297 Chirality : 0.042 0.195 5400 Planarity : 0.004 0.060 6291 Dihedral : 8.442 110.299 5110 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 0.86 % Allowed : 11.86 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.13), residues: 4377 helix: 2.06 (0.12), residues: 2006 sheet: 0.63 (0.20), residues: 646 loop : 0.68 (0.16), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.013 0.001 TYR D 134 PHE 0.018 0.001 PHE F 771 TRP 0.009 0.001 TRP A 454 HIS 0.005 0.001 HIS A 735 Details of bonding type rmsd covalent geometry : bond 0.00324 (35524) covalent geometry : angle 0.60191 (48034) hydrogen bonds : bond 0.03323 ( 1605) hydrogen bonds : angle 4.42771 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7717.11 seconds wall clock time: 133 minutes 32.68 seconds (8012.68 seconds total)