Starting phenix.real_space_refine on Mon Jul 6 11:07:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ln2_23446/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_2026/7ln2_23446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ln2_23446/07_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-6108/lib/python3.11/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: 8.16, per 1000 atoms: 0.23 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.28 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: 7.88 Time building geometry restraints manager: 3.71 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: 21257 29.31 - 58.61: 615 58.61 - 87.92: 51 87.92 - 117.23: 8 117.23 - 146.53: 5 Dihedral angle restraints: 21936 sinusoidal: 9167 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 21933 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.560 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 : 13.471 146.534 13648 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/Z covalent geometry : bond 0.00396 / 0.17 (35524) covalent geometry : angle 0.65035 / 0.35 (48034) hydrogen bonds : bond 0.17779 / 12.15 ( 1605) hydrogen bonds : angle 6.29493 / 4.49 ( 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 : 1.326 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: 0.2349 time to fit residues: 92.5729 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 : 1.132 ------------------------------------------------------------------------------- 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... 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 = 0.076640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.045991 restraints weight = 226778.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046092 restraints weight = 129053.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046487 restraints weight = 90345.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.046875 restraints weight = 76502.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046952 restraints weight = 69510.475| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35524 Z= 0.223 Angle : 0.653 9.605 48034 Z= 0.332 Chirality : 0.044 0.201 5400 Planarity : 0.005 0.059 6291 Dihedral : 6.699 137.092 4893 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.58 % Favored : 98.36 % Rotamer: Outliers : 0.43 % Allowed : 5.51 % 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: 1.72 (0.13), residues: 4377 helix: 1.77 (0.11), residues: 1994 sheet: 0.91 (0.19), residues: 672 loop : 0.64 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 708 TYR 0.015 0.001 TYR B 495 PHE 0.021 0.002 PHE A 742 TRP 0.015 0.002 TRP A 454 HIS 0.012 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (35524) covalent geometry : angle 0.65275 / 0.33 (48034) hydrogen bonds : bond 0.04348 / 2.91 ( 1605) hydrogen bonds : angle 5.06987 / 3.63 ( 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 167 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9334 (pmm) cc_final: 0.8921 (pmm) REVERT: B 344 MET cc_start: 0.8167 (mpp) cc_final: 0.7892 (mpp) REVERT: B 550 MET cc_start: 0.9050 (ppp) cc_final: 0.8362 (ppp) REVERT: C 84 MET cc_start: 0.9186 (tpt) cc_final: 0.8959 (tpp) REVERT: C 427 MET cc_start: 0.8014 (tpt) cc_final: 0.7620 (tpp) REVERT: D 46 MET cc_start: 0.5601 (mpp) cc_final: 0.5383 (ptp) REVERT: D 388 MET cc_start: 0.8279 (ptp) cc_final: 0.8005 (ptp) REVERT: E 608 MET cc_start: 0.9381 (ptm) cc_final: 0.9172 (ptm) REVERT: E 678 MET cc_start: 0.9081 (mmm) cc_final: 0.8859 (mmm) REVERT: F 219 MET cc_start: 0.8634 (mmp) cc_final: 0.8408 (mmt) REVERT: F 449 MET cc_start: 0.8825 (tpp) cc_final: 0.8587 (tpp) outliers start: 16 outliers final: 11 residues processed: 161 average time/residue: 0.2040 time to fit residues: 55.9078 Evaluate side-chains 149 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 4.9990 chunk 301 optimal weight: 40.0000 chunk 172 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 chunk 364 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 76 optimal weight: 50.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** 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 = 0.3867 r_free = 0.3867 target = 0.078173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047864 restraints weight = 224610.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047165 restraints weight = 129627.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.047696 restraints weight = 91358.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047904 restraints weight = 76331.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.048135 restraints weight = 69781.372| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35524 Z= 0.124 Angle : 0.553 9.580 48034 Z= 0.277 Chirality : 0.042 0.188 5400 Planarity : 0.004 0.051 6291 Dihedral : 6.370 127.466 4893 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer: Outliers : 0.67 % Allowed : 6.96 % Favored : 92.36 % 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: 1.88 (0.13), residues: 4377 helix: 1.96 (0.12), residues: 1988 sheet: 0.88 (0.19), residues: 660 loop : 0.71 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 772 TYR 0.012 0.001 TYR F 495 PHE 0.015 0.001 PHE A 742 TRP 0.013 0.001 TRP F 476 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (35524) covalent geometry : angle 0.55300 / 0.28 (48034) hydrogen bonds : bond 0.03830 / 2.57 ( 1605) hydrogen bonds : angle 4.63482 / 3.32 ( 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 168 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9248 (pmm) cc_final: 0.8892 (pmm) REVERT: B 344 MET cc_start: 0.8143 (mpp) cc_final: 0.7850 (mpp) REVERT: B 442 MET cc_start: 0.8946 (mmm) cc_final: 0.8119 (mmm) REVERT: B 550 MET cc_start: 0.9078 (ppp) cc_final: 0.8394 (ppp) REVERT: C 84 MET cc_start: 0.9369 (tpt) cc_final: 0.9102 (tpp) REVERT: C 427 MET cc_start: 0.8244 (tpt) cc_final: 0.7916 (tpp) REVERT: D 332 MET cc_start: 0.9033 (ttm) cc_final: 0.8810 (ttm) REVERT: E 678 MET cc_start: 0.9077 (mmm) cc_final: 0.8863 (mmm) REVERT: F 678 MET cc_start: 0.9357 (mtp) cc_final: 0.9142 (mtp) outliers start: 25 outliers final: 11 residues processed: 160 average time/residue: 0.1890 time to fit residues: 52.3358 Evaluate side-chains 144 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 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 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: 30.0000 chunk 218 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 223 optimal weight: 30.0000 chunk 179 optimal weight: 20.0000 chunk 248 optimal weight: 0.5980 chunk 254 optimal weight: 10.0000 chunk 358 optimal weight: 0.5980 chunk 309 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 GLN A 692 GLN B 296 ASN B 641 GLN C 458 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.076956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050560 restraints weight = 226321.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.051485 restraints weight = 138614.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051753 restraints weight = 87903.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.051154 restraints weight = 86955.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051136 restraints weight = 70960.453| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2143 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= 0.166 Angle : 0.570 9.723 48034 Z= 0.283 Chirality : 0.042 0.185 5400 Planarity : 0.004 0.053 6291 Dihedral : 6.201 119.843 4893 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.22 % Rotamer: Outliers : 0.86 % Allowed : 8.17 % Favored : 90.97 % 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: 1.92 (0.13), residues: 4377 helix: 2.02 (0.12), residues: 1986 sheet: 0.86 (0.19), residues: 639 loop : 0.70 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 638 TYR 0.016 0.001 TYR D 134 PHE 0.016 0.001 PHE F 674 TRP 0.008 0.001 TRP F 476 HIS 0.004 0.001 HIS C 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (35524) covalent geometry : angle 0.56988 / 0.28 (48034) hydrogen bonds : bond 0.03595 / 2.41 ( 1605) hydrogen bonds : angle 4.56472 / 3.27 ( 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 168 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9309 (pmm) cc_final: 0.8979 (pmm) REVERT: B 344 MET cc_start: 0.8161 (mpp) cc_final: 0.7887 (mpp) REVERT: B 421 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: B 442 MET cc_start: 0.8911 (mmm) cc_final: 0.8189 (mmm) REVERT: C 388 MET cc_start: 0.8590 (mtt) cc_final: 0.8177 (mtm) REVERT: C 427 MET cc_start: 0.8054 (tpt) cc_final: 0.7792 (tpp) REVERT: D 46 MET cc_start: 0.5178 (ptp) cc_final: 0.3962 (ptp) REVERT: D 332 MET cc_start: 0.8854 (ttm) cc_final: 0.8449 (ttm) REVERT: E 335 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9051 (tp) REVERT: E 678 MET cc_start: 0.9077 (mmm) cc_final: 0.8862 (mmm) outliers start: 32 outliers final: 13 residues processed: 159 average time/residue: 0.1967 time to fit residues: 54.6072 Evaluate side-chains 144 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 737 GLU 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 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: 5.9990 chunk 375 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 2 optimal weight: 40.0000 chunk 251 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 258 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 300 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 641 GLN ** A 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 473 GLN C 533 ASN D 215 GLN ** 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 401 ASN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.089113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058628 restraints weight = 113644.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058340 restraints weight = 107626.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.058134 restraints weight = 98118.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057880 restraints weight = 98133.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.057821 restraints weight = 96944.978| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 35524 Z= 0.303 Angle : 0.702 10.039 48034 Z= 0.354 Chirality : 0.044 0.200 5400 Planarity : 0.005 0.056 6291 Dihedral : 6.451 117.293 4893 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Rotamer: Outliers : 0.86 % Allowed : 9.81 % Favored : 89.33 % 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: 1.48 (0.13), residues: 4377 helix: 1.61 (0.11), residues: 2016 sheet: 0.72 (0.19), residues: 648 loop : 0.49 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 772 TYR 0.016 0.001 TYR A 495 PHE 0.022 0.002 PHE F 674 TRP 0.011 0.002 TRP D 454 HIS 0.008 0.002 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.30 (35524) covalent geometry : angle 0.70238 / 0.35 (48034) hydrogen bonds : bond 0.04043 / 2.70 ( 1605) hydrogen bonds : angle 4.91581 / 3.52 ( 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 165 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8997 (pmm) cc_final: 0.8591 (pmm) REVERT: B 344 MET cc_start: 0.8116 (mpp) cc_final: 0.7831 (mpp) REVERT: B 421 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8741 (tm-30) REVERT: B 442 MET cc_start: 0.8722 (mmm) cc_final: 0.7988 (mmm) REVERT: B 737 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8727 (mp0) REVERT: B 740 MET cc_start: 0.8751 (ppp) cc_final: 0.8551 (ppp) REVERT: C 388 MET cc_start: 0.8579 (mtt) cc_final: 0.8178 (mtt) REVERT: C 427 MET cc_start: 0.8350 (tpt) cc_final: 0.7805 (tpp) REVERT: D 46 MET cc_start: 0.6169 (ptp) cc_final: 0.5293 (ptp) REVERT: D 95 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8096 (mmp80) REVERT: E 158 MET cc_start: 0.0625 (pmm) cc_final: 0.0329 (pmm) REVERT: E 173 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6735 (m-80) REVERT: E 678 MET cc_start: 0.9156 (mmm) cc_final: 0.8876 (mmm) REVERT: F 449 MET cc_start: 0.8886 (tpt) cc_final: 0.8680 (tpt) outliers start: 32 outliers final: 15 residues processed: 155 average time/residue: 0.1960 time to fit residues: 52.5812 Evaluate side-chains 145 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 737 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 41 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 231 optimal weight: 8.9990 chunk 394 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 18 optimal weight: 0.0050 chunk 421 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN ** 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** ** 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 401 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 = 0.3836 r_free = 0.3836 target = 0.084671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057014 restraints weight = 128916.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057599 restraints weight = 103880.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057879 restraints weight = 92064.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058348 restraints weight = 86064.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058426 restraints weight = 81197.737| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 35524 Z= 0.109 Angle : 0.566 9.608 48034 Z= 0.281 Chirality : 0.043 0.198 5400 Planarity : 0.004 0.060 6291 Dihedral : 5.960 113.106 4893 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.29 % Rotamer: Outliers : 0.78 % Allowed : 10.70 % Favored : 88.52 % 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: 1.87 (0.13), residues: 4377 helix: 2.01 (0.12), residues: 1986 sheet: 0.87 (0.20), residues: 626 loop : 0.63 (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 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (35524) covalent geometry : angle 0.56630 / 0.28 (48034) hydrogen bonds : bond 0.03378 / 2.26 ( 1605) hydrogen bonds : angle 4.39741 / 3.15 ( 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 159 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.9192 (pmm) cc_final: 0.8781 (pmm) REVERT: A 427 MET cc_start: 0.8942 (mmt) cc_final: 0.8665 (pmm) REVERT: A 611 MET cc_start: 0.7385 (mmt) cc_final: 0.6481 (mmm) REVERT: B 344 MET cc_start: 0.8240 (mpp) cc_final: 0.7976 (mpp) REVERT: B 421 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8827 (tm-30) REVERT: B 442 MET cc_start: 0.8995 (mmm) cc_final: 0.8051 (mmm) REVERT: C 388 MET cc_start: 0.8423 (mtt) cc_final: 0.8009 (mtm) REVERT: C 427 MET cc_start: 0.7854 (tpt) cc_final: 0.7606 (tpp) REVERT: D 46 MET cc_start: 0.6047 (ptp) cc_final: 0.5498 (ptp) REVERT: D 95 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8142 (mmp80) REVERT: E 158 MET cc_start: 0.1212 (pmm) cc_final: 0.0913 (pmm) REVERT: E 173 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: E 335 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9062 (tp) REVERT: E 757 MET cc_start: 0.9213 (ptp) cc_final: 0.9012 (ptp) REVERT: F 215 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9021 (mt0) REVERT: F 449 MET cc_start: 0.8863 (tpt) cc_final: 0.8539 (tpt) outliers start: 29 outliers final: 13 residues processed: 151 average time/residue: 0.1934 time to fit residues: 50.8843 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 : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 737 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 611 MET 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 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: 10.0000 chunk 176 optimal weight: 6.9990 chunk 308 optimal weight: 30.0000 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 387 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3812 r_free = 0.3812 target = 0.090337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066634 restraints weight = 208046.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066243 restraints weight = 147502.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.066539 restraints weight = 104216.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066784 restraints weight = 88917.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066750 restraints weight = 85136.358| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35524 Z= 0.229 Angle : 0.635 13.133 48034 Z= 0.315 Chirality : 0.042 0.185 5400 Planarity : 0.004 0.059 6291 Dihedral : 5.973 110.963 4893 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 11.00 % Favored : 88.17 % 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: 1.81 (0.13), residues: 4377 helix: 1.95 (0.12), residues: 2009 sheet: 0.83 (0.20), residues: 627 loop : 0.60 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 89 TYR 0.014 0.001 TYR D 134 PHE 0.015 0.001 PHE F 771 TRP 0.008 0.001 TRP A 476 HIS 0.005 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (35524) covalent geometry : angle 0.63456 / 0.31 (48034) hydrogen bonds : bond 0.03517 / 2.35 ( 1605) hydrogen bonds : angle 4.61546 / 3.30 ( 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 155 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9518 (mpp) cc_final: 0.9208 (mpp) REVERT: A 344 MET cc_start: 0.9165 (pmm) cc_final: 0.8755 (pmm) REVERT: B 344 MET cc_start: 0.8216 (mpp) cc_final: 0.7819 (mpp) REVERT: B 421 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8886 (tm-30) REVERT: B 442 MET cc_start: 0.8900 (mmm) cc_final: 0.8063 (mmm) REVERT: C 388 MET cc_start: 0.8479 (mtt) cc_final: 0.8161 (mtt) REVERT: C 427 MET cc_start: 0.8196 (tpt) cc_final: 0.7676 (tpp) REVERT: C 449 MET cc_start: 0.9120 (tpp) cc_final: 0.8882 (tmm) REVERT: C 740 MET cc_start: 0.9122 (ppp) cc_final: 0.8764 (ppp) REVERT: D 46 MET cc_start: 0.6235 (ptp) cc_final: 0.5728 (ptp) REVERT: D 95 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8317 (mmp80) REVERT: E 84 MET cc_start: 0.3240 (tpt) cc_final: 0.3009 (tpp) REVERT: E 158 MET cc_start: 0.1949 (pmm) cc_final: 0.1675 (pmm) REVERT: E 173 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: F 215 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (mt0) REVERT: F 344 MET cc_start: 0.9597 (pmm) cc_final: 0.9388 (pmm) outliers start: 31 outliers final: 22 residues processed: 146 average time/residue: 0.1995 time to fit residues: 51.0050 Evaluate side-chains 146 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 574 LEU Chi-restraints excluded: chain B residue 737 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 41 LEU Chi-restraints excluded: chain D residue 42 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 270 optimal weight: 0.0870 chunk 104 optimal weight: 0.4980 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 299 optimal weight: 30.0000 chunk 103 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 360 optimal weight: 6.9990 chunk 430 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 538 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** E 348 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.075892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.049559 restraints weight = 226962.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.050225 restraints weight = 137067.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050214 restraints weight = 88883.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.050133 restraints weight = 93670.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050176 restraints weight = 80833.524| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 35524 Z= 0.102 Angle : 0.571 12.151 48034 Z= 0.279 Chirality : 0.042 0.184 5400 Planarity : 0.004 0.059 6291 Dihedral : 5.774 110.914 4893 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.17 % Rotamer: Outliers : 0.75 % Allowed : 11.32 % Favored : 87.93 % 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: 1.98 (0.13), residues: 4377 helix: 2.11 (0.12), residues: 1992 sheet: 0.90 (0.20), residues: 626 loop : 0.67 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.014 0.001 TYR D 134 PHE 0.016 0.001 PHE E 758 TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (35524) covalent geometry : angle 0.57076 / 0.28 (48034) hydrogen bonds : bond 0.03237 / 2.16 ( 1605) hydrogen bonds : angle 4.32589 / 3.09 ( 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 154 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9474 (mpp) cc_final: 0.9101 (mpp) REVERT: A 344 MET cc_start: 0.9258 (pmm) cc_final: 0.8869 (pmm) REVERT: B 332 MET cc_start: 0.9218 (ttm) cc_final: 0.8837 (tmm) REVERT: B 344 MET cc_start: 0.8196 (mpp) cc_final: 0.7922 (mpp) REVERT: B 421 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8847 (tm-30) REVERT: B 442 MET cc_start: 0.8783 (mmm) cc_final: 0.8141 (mmm) REVERT: C 388 MET cc_start: 0.8298 (mtt) cc_final: 0.7918 (mtm) REVERT: C 427 MET cc_start: 0.8374 (tpt) cc_final: 0.7853 (tpp) REVERT: C 449 MET cc_start: 0.9032 (tpp) cc_final: 0.8799 (tmm) REVERT: C 740 MET cc_start: 0.9159 (ppp) cc_final: 0.8822 (ppp) REVERT: D 46 MET cc_start: 0.6129 (ptp) cc_final: 0.5523 (ptp) REVERT: D 95 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8275 (mmp80) REVERT: E 84 MET cc_start: 0.3200 (tpt) cc_final: 0.2866 (tpp) REVERT: E 158 MET cc_start: 0.2976 (pmm) cc_final: 0.2749 (pmm) REVERT: E 173 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6723 (m-80) REVERT: E 335 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9179 (tp) REVERT: E 427 MET cc_start: 0.9339 (ptt) cc_final: 0.9111 (ppp) REVERT: E 449 MET cc_start: 0.8975 (mmm) cc_final: 0.8734 (mmm) REVERT: F 344 MET cc_start: 0.9550 (pmm) cc_final: 0.9337 (pmm) outliers start: 28 outliers final: 15 residues processed: 147 average time/residue: 0.1959 time to fit residues: 50.5168 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 737 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 42 SER 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 E residue 728 VAL Chi-restraints excluded: chain F residue 158 MET 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: 9.9990 chunk 410 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 367 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.074110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.046373 restraints weight = 232246.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.044480 restraints weight = 124713.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044930 restraints weight = 91207.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.045163 restraints weight = 74868.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.045161 restraints weight = 66026.537| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3327 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= 0.200 Angle : 0.619 13.715 48034 Z= 0.305 Chirality : 0.042 0.183 5400 Planarity : 0.004 0.060 6291 Dihedral : 5.817 111.275 4893 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % Rotamer: Outliers : 0.81 % Allowed : 11.48 % Favored : 87.71 % 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: 2.02 (0.12), residues: 2013 sheet: 0.89 (0.20), residues: 625 loop : 0.63 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 638 TYR 0.014 0.001 TYR D 134 PHE 0.018 0.001 PHE F 771 TRP 0.007 0.001 TRP A 454 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (35524) covalent geometry : angle 0.61915 / 0.30 (48034) hydrogen bonds : bond 0.03379 / 2.26 ( 1605) hydrogen bonds : angle 4.50883 / 3.23 ( 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: 30 poor density : 124 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9485 (mpp) cc_final: 0.8940 (mpp) REVERT: A 344 MET cc_start: 0.9145 (pmm) cc_final: 0.8734 (pmm) REVERT: A 611 MET cc_start: 0.6981 (mmt) cc_final: 0.6640 (mmm) REVERT: B 344 MET cc_start: 0.8169 (mpp) cc_final: 0.7862 (mpp) REVERT: B 388 MET cc_start: 0.8409 (pmm) cc_final: 0.8126 (pmm) REVERT: B 421 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: B 442 MET cc_start: 0.8956 (mmm) cc_final: 0.8143 (mmm) REVERT: C 388 MET cc_start: 0.8434 (mtt) cc_final: 0.8174 (mtt) REVERT: C 427 MET cc_start: 0.8200 (tpt) cc_final: 0.7653 (tpp) REVERT: C 449 MET cc_start: 0.9150 (tpp) cc_final: 0.8916 (tmm) REVERT: C 740 MET cc_start: 0.9164 (ppp) cc_final: 0.8807 (ppp) REVERT: D 46 MET cc_start: 0.6248 (ptp) cc_final: 0.5682 (ptp) REVERT: D 275 MET cc_start: 0.9321 (mmm) cc_final: 0.9001 (mmm) REVERT: E 335 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9108 (tp) REVERT: E 449 MET cc_start: 0.8997 (mmm) cc_final: 0.8795 (mmm) REVERT: F 344 MET cc_start: 0.9604 (pmm) cc_final: 0.9371 (pmm) outliers start: 30 outliers final: 20 residues processed: 147 average time/residue: 0.1942 time to fit residues: 50.3805 Evaluate side-chains 144 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 737 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 SER 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 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: 8.9990 chunk 36 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 16 optimal weight: 0.0970 chunk 307 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 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 = 0.074682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.044197 restraints weight = 231240.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.043974 restraints weight = 129984.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044407 restraints weight = 92293.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044518 restraints weight = 77829.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044735 restraints weight = 72728.295| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3405 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= 0.133 Angle : 0.595 16.909 48034 Z= 0.291 Chirality : 0.042 0.265 5400 Planarity : 0.004 0.060 6291 Dihedral : 5.752 110.202 4893 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.01 % Favored : 97.92 % Rotamer: Outliers : 0.67 % Allowed : 11.70 % Favored : 87.63 % 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: 1.96 (0.13), residues: 4377 helix: 2.07 (0.12), residues: 2003 sheet: 0.87 (0.20), residues: 627 loop : 0.69 (0.16), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 638 TYR 0.013 0.001 TYR D 134 PHE 0.016 0.001 PHE F 771 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (35524) covalent geometry : angle 0.59547 / 0.29 (48034) hydrogen bonds : bond 0.03263 / 2.18 ( 1605) hydrogen bonds : angle 4.40372 / 3.15 ( 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 148 residues out of total 3770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9460 (mpp) cc_final: 0.9139 (mpp) REVERT: A 344 MET cc_start: 0.9169 (pmm) cc_final: 0.8733 (pmm) REVERT: A 427 MET cc_start: 0.9206 (mmm) cc_final: 0.8932 (pmm) REVERT: A 611 MET cc_start: 0.6706 (mmt) cc_final: 0.6382 (mmm) REVERT: B 332 MET cc_start: 0.9314 (ttm) cc_final: 0.8883 (tmm) REVERT: B 344 MET cc_start: 0.8172 (mpp) cc_final: 0.7851 (mpp) REVERT: B 388 MET cc_start: 0.8537 (pmm) cc_final: 0.8242 (pmm) REVERT: B 421 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8834 (tm-30) REVERT: B 442 MET cc_start: 0.8928 (mmm) cc_final: 0.8143 (mmm) REVERT: C 388 MET cc_start: 0.8342 (mtt) cc_final: 0.7953 (mtm) REVERT: C 427 MET cc_start: 0.8222 (tpt) cc_final: 0.7696 (tpp) REVERT: C 449 MET cc_start: 0.9138 (tpp) cc_final: 0.8902 (tmm) REVERT: C 740 MET cc_start: 0.9160 (ppp) cc_final: 0.8815 (ppp) REVERT: D 46 MET cc_start: 0.6306 (ptp) cc_final: 0.5739 (ptp) REVERT: D 95 ARG cc_start: 0.8721 (mtt180) cc_final: 0.7751 (mmp80) REVERT: E 335 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9129 (tp) REVERT: F 344 MET cc_start: 0.9578 (pmm) cc_final: 0.9352 (pmm) outliers start: 25 outliers final: 22 residues processed: 141 average time/residue: 0.1811 time to fit residues: 44.5882 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 : 1.389 ------------------------------------------------------------------------------- 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 737 GLU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 42 SER 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 348 ASN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 3 optimal weight: 10.0000 chunk 423 optimal weight: 3.9990 chunk 391 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 283 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 200 optimal weight: 0.0570 chunk 83 optimal weight: 6.9990 chunk 382 optimal weight: 20.0000 chunk 399 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 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 = 0.3790 r_free = 0.3790 target = 0.074626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.047018 restraints weight = 230377.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045132 restraints weight = 122923.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045527 restraints weight = 88998.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045772 restraints weight = 74768.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046008 restraints weight = 67828.112| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 35524 Z= 0.168 Angle : 0.692 59.200 48034 Z= 0.369 Chirality : 0.044 0.782 5400 Planarity : 0.004 0.060 6291 Dihedral : 5.784 110.211 4893 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.90 % Rotamer: Outliers : 0.70 % Allowed : 11.72 % Favored : 87.58 % Cbeta Deviations : 0.02 % 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: 1.95 (0.13), residues: 4377 helix: 2.06 (0.12), residues: 2003 sheet: 0.88 (0.20), residues: 626 loop : 0.69 (0.16), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 638 TYR 0.012 0.001 TYR D 134 PHE 0.015 0.001 PHE F 771 TRP 0.007 0.001 TRP A 476 HIS 0.004 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (35524) covalent geometry : angle 0.69204 / 0.37 (48034) hydrogen bonds : bond 0.03291 / 2.21 ( 1605) hydrogen bonds : angle 4.40944 / 3.15 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7437.12 seconds wall clock time: 128 minutes 36.69 seconds (7716.69 seconds total)