Starting phenix.real_space_refine on Mon Jul 6 04:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds3_27682/07_2026/8ds3_27682.map" } resolution = 3.07 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= 0.021 sd= 0.072 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 154 5.16 5 C 21312 2.51 5 N 5357 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32601 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "C" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 5915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5915 Classifications: {'peptide': 717} Link IDs: {'PTRANS': 27, 'TRANS': 689} Chain breaks: 2 Chain: "F" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5751 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 24, 'TRANS': 679} Chain breaks: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 115 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PEE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.81, per 1000 atoms: 0.18 Number of scatterers: 32601 At special positions: 0 Unit cell: (140.432, 137.288, 194.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 154 16.00 P 9 15.00 O 5769 8.00 N 5357 7.00 C 21312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.02 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7542 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 23 sheets defined 52.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.018A pdb=" N ILE A 19 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 119 through 141 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.668A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.912A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.840A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 315 through 345 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 370 through 383 removed outlier: 3.527A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.109A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 removed outlier: 3.507A pdb=" N TRP A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.723A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 509 through 515 removed outlier: 3.635A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 515 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 4.238A pdb=" N GLY A 539 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 541 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.911A pdb=" N LYS A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 589 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.509A pdb=" N GLN A 636 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.627A pdb=" N ILE A 658 " --> pdb=" O PRO A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.568A pdb=" N CYS A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 removed outlier: 3.770A pdb=" N ILE A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 730 removed outlier: 3.936A pdb=" N PHE A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 795 through 808 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.595A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.640A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.789A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.606A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 314 through 343 removed outlier: 3.906A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.208A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.844A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.854A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 4.280A pdb=" N SER B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.532A pdb=" N ASP B 538 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.684A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.637A pdb=" N CYS B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.508A pdb=" N GLY B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.775A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.557A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 16 through 21 removed outlier: 4.010A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.705A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.690A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.270A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 removed outlier: 3.537A pdb=" N ALA C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.068A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.634A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.755A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.247A pdb=" N PHE C 611 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.526A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.823A pdb=" N LEU C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.751A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.662A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.763A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 807 Processing helix chain 'D' and resid 16 through 21 removed outlier: 4.254A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 117 Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.565A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.005A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.905A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.653A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 258 through 286 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.942A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.006A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.766A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.761A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 258 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 315 through 343 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 392 removed outlier: 4.005A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.589A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.056A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.702A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.629A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.560A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.344A pdb=" N VAL F 19 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.960A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 3.707A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 3.882A pdb=" N SER F 153 " --> pdb=" O PRO F 149 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.335A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 253 removed outlier: 3.627A pdb=" N GLU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 284 removed outlier: 3.514A pdb=" N ALA F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 343 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 368 through 381 Processing helix chain 'F' and resid 382 through 393 removed outlier: 3.718A pdb=" N LYS F 386 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.547A pdb=" N TRP F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 437 through 443 removed outlier: 3.921A pdb=" N PHE F 441 " --> pdb=" O PRO F 437 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 443 " --> pdb=" O THR F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 3.946A pdb=" N ILE F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 492 Processing helix chain 'F' and resid 509 through 513 removed outlier: 3.833A pdb=" N LEU F 513 " --> pdb=" O MET F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 538 removed outlier: 3.801A pdb=" N SER F 537 " --> pdb=" O THR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.711A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 587 Processing helix chain 'F' and resid 605 through 611 removed outlier: 4.098A pdb=" N PHE F 609 " --> pdb=" O PRO F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 636 removed outlier: 3.524A pdb=" N SER F 632 " --> pdb=" O GLU F 629 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 634 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.934A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 659 " --> pdb=" O ILE F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 removed outlier: 3.699A pdb=" N ILE F 702 " --> pdb=" O PRO F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 Processing helix chain 'F' and resid 745 through 749 removed outlier: 3.540A pdb=" N ILE F 748 " --> pdb=" O SER F 745 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY F 749 " --> pdb=" O PRO F 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 745 through 749' Processing helix chain 'F' and resid 768 through 772 removed outlier: 4.126A pdb=" N LEU F 771 " --> pdb=" O PRO F 768 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY F 772 " --> pdb=" O PRO F 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 768 through 772' Processing helix chain 'F' and resid 785 through 790 Processing helix chain 'F' and resid 793 through 802 removed outlier: 3.816A pdb=" N ALA F 802 " --> pdb=" O GLU F 798 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.720A pdb=" N VAL A 60 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 94 " --> pdb=" O VAL A 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.638A pdb=" N LEU A 428 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 474 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS A 501 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 521 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS A 552 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 523 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU A 572 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A 599 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE A 574 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 618 through 620 Processing sheet with id=AA6, first strand: chain 'A' and resid 666 through 668 removed outlier: 7.012A pdb=" N LEU A 667 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 735 through 737 removed outlier: 6.819A pdb=" N LEU A 736 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE A 759 " --> pdb=" O VAL A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.965A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 550 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 523 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 552 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 736 through 737 removed outlier: 6.611A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS C 522 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 573 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 645 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.032A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 735 through 736 removed outlier: 8.155A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 351 removed outlier: 3.721A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 56 removed outlier: 3.556A pdb=" N LEU E 55 " --> pdb=" O ARG E 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.701A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 449 " --> pdb=" O CYS F 473 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET F 570 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL F 597 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL F 572 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU F 594 " --> pdb=" O ASP F 618 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LYS F 620 " --> pdb=" O LEU F 594 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU F 596 " --> pdb=" O LYS F 620 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU F 617 " --> pdb=" O LYS F 643 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU F 688 " --> pdb=" O SER F 712 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 457 through 458 removed outlier: 6.568A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 1439 hydrogen bonds defined for protein. 3948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.18 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6102 1.33 - 1.45: 7878 1.45 - 1.57: 19088 1.57 - 1.70: 14 1.70 - 1.82: 225 Bond restraints: 33307 Sorted by residual: bond pdb=" C10 PEE A 902 " pdb=" O4 PEE A 902 " ideal model delta sigma weight residual 1.206 1.358 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" C10 PEE E 902 " pdb=" O4 PEE E 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE D 902 " pdb=" O4 PEE D 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C10 PEE E 903 " pdb=" O4 PEE E 903 " ideal model delta sigma weight residual 1.206 1.356 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 33302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 44180 2.77 - 5.54: 628 5.54 - 8.31: 123 8.31 - 11.08: 30 11.08 - 13.85: 16 Bond angle restraints: 44977 Sorted by residual: angle pdb=" O1P PEE F 904 " pdb=" P PEE F 904 " pdb=" O2P PEE F 904 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.26 -13.83 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O1P PEE D 904 " pdb=" P PEE D 904 " pdb=" O2P PEE D 904 " ideal model delta sigma weight residual 119.43 133.22 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE C 901 " pdb=" P PEE C 901 " pdb=" O2P PEE C 901 " ideal model delta sigma weight residual 119.43 133.20 -13.77 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O1P PEE A 901 " pdb=" P PEE A 901 " pdb=" O2P PEE A 901 " ideal model delta sigma weight residual 119.43 133.18 -13.75 3.00e+00 1.11e-01 2.10e+01 ... (remaining 44972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 19607 35.96 - 71.93: 540 71.93 - 107.89: 20 107.89 - 143.85: 8 143.85 - 179.82: 14 Dihedral angle restraints: 20189 sinusoidal: 8607 harmonic: 11582 Sorted by residual: dihedral pdb=" CB CYS B 113 " pdb=" SG CYS B 113 " pdb=" SG CYS B 295 " pdb=" CB CYS B 295 " ideal model delta sinusoidal sigma weight residual 93.00 50.48 42.52 1 1.00e+01 1.00e-02 2.52e+01 dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 20186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4898 0.098 - 0.195: 195 0.195 - 0.293: 3 0.293 - 0.390: 3 0.390 - 0.488: 8 Chirality restraints: 5107 Sorted by residual: chirality pdb=" CB ILE A 629 " pdb=" CA ILE A 629 " pdb=" CG1 ILE A 629 " pdb=" CG2 ILE A 629 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C2 PEE B 904 " pdb=" C1 PEE B 904 " pdb=" C3 PEE B 904 " pdb=" O2 PEE B 904 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C2 PEE C 901 " pdb=" C1 PEE C 901 " pdb=" C3 PEE C 901 " pdb=" O2 PEE C 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.74 0.41 2.00e-01 2.50e+01 4.22e+00 ... (remaining 5104 not shown) Planarity restraints: 5516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 475 " -0.032 2.00e-02 2.50e+03 2.93e-02 2.15e+01 pdb=" CG TRP A 475 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP A 475 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 475 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 475 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 475 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 475 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 475 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 475 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 725 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " -0.046 5.00e-02 4.00e+02 ... (remaining 5513 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3254 2.75 - 3.29: 32689 3.29 - 3.82: 56283 3.82 - 4.36: 68614 4.36 - 4.90: 113233 Nonbonded interactions: 274073 Sorted by model distance: nonbonded pdb=" O SER E 395 " pdb=" OG SER E 398 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" O MET F 300 " model vdw 2.213 3.040 nonbonded pdb=" O SER A 166 " pdb=" OG1 THR A 169 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 166 " pdb=" OG1 THR D 169 " model vdw 2.233 3.040 nonbonded pdb=" O SER B 166 " pdb=" OG1 THR B 169 " model vdw 2.233 3.040 ... (remaining 274068 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 15 through 901 or (resid 902 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'B' and resid 15 through 903) selection = (chain 'C' and (resid 15 through 901 or (resid 902 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) selection = (chain 'E' and (resid 15 through 901 or (resid 902 through 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name O2 \ or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.380 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 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 : 0.005 0.152 33324 Z= 0.270 Angle : 0.898 13.848 45011 Z= 0.459 Chirality : 0.048 0.488 5107 Planarity : 0.006 0.093 5516 Dihedral : 16.893 179.817 12596 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 18.38 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.13), residues: 3852 helix: -0.29 (0.12), residues: 1852 sheet: -1.57 (0.29), residues: 358 loop : -1.33 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 389 TYR 0.053 0.002 TYR F 687 PHE 0.041 0.002 PHE F 488 TRP 0.080 0.003 TRP A 475 HIS 0.011 0.001 HIS E 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.27 (33307) covalent geometry : angle 0.89772 / 0.46 (44977) SS BOND : bond 0.00289 / 0.18 ( 17) SS BOND : angle 0.75448 / 0.46 ( 34) hydrogen bonds : bond 0.15472 / 10.05 ( 1439) hydrogen bonds : angle 6.80345 / 4.83 ( 3948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 333 time to evaluate : 1.173 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: C 438 ILE cc_start: 0.7420 (pt) cc_final: 0.7126 (pt) REVERT: F 145 TRP cc_start: 0.5443 (t60) cc_final: 0.5105 (t60) outliers start: 10 outliers final: 5 residues processed: 339 average time/residue: 0.1872 time to fit residues: 104.1297 Evaluate side-chains 298 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 293 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain D residue 324 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 GLN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN E 532 ASN E 694 HIS F 402 GLN F 424 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.160935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.113496 restraints weight = 72173.747| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.29 r_work: 0.3534 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33324 Z= 0.186 Angle : 0.598 12.236 45011 Z= 0.306 Chirality : 0.042 0.290 5107 Planarity : 0.004 0.065 5516 Dihedral : 12.709 177.791 4599 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.77 % Allowed : 17.50 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.86 (0.14), residues: 3852 helix: 0.27 (0.12), residues: 1886 sheet: -1.32 (0.30), residues: 350 loop : -1.34 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 492 TYR 0.023 0.002 TYR F 511 PHE 0.021 0.002 PHE D 324 TRP 0.027 0.002 TRP A 475 HIS 0.006 0.001 HIS A 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (33307) covalent geometry : angle 0.59826 / 0.31 (44977) SS BOND : bond 0.00395 / 0.24 ( 17) SS BOND : angle 0.75468 / 0.47 ( 34) hydrogen bonds : bond 0.04418 / 2.92 ( 1439) hydrogen bonds : angle 5.08196 / 3.61 ( 3948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 324 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7443 (pp20) REVERT: A 434 MET cc_start: 0.8025 (mpp) cc_final: 0.7817 (mpp) REVERT: A 501 LYS cc_start: 0.8899 (tttt) cc_final: 0.8554 (tptt) REVERT: B 239 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7671 (mm110) REVERT: B 729 GLN cc_start: 0.7950 (tt0) cc_final: 0.7694 (tt0) REVERT: C 509 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7712 (Cg_exo) REVERT: C 590 MET cc_start: 0.4198 (mmm) cc_final: 0.3936 (mmm) REVERT: E 29 ASP cc_start: 0.8342 (t0) cc_final: 0.7932 (m-30) REVERT: E 235 LYS cc_start: 0.8559 (mmpt) cc_final: 0.8172 (mmtt) REVERT: E 239 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: E 263 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7778 (tp) REVERT: E 438 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8040 (tt) REVERT: E 477 TYR cc_start: 0.7558 (m-80) cc_final: 0.7172 (m-80) REVERT: E 499 HIS cc_start: 0.7262 (m170) cc_final: 0.6962 (m-70) REVERT: F 144 PHE cc_start: 0.7926 (t80) cc_final: 0.7666 (t80) REVERT: F 175 LEU cc_start: 0.8753 (tp) cc_final: 0.8496 (mt) REVERT: F 588 MET cc_start: 0.7406 (mmp) cc_final: 0.6665 (mmm) REVERT: F 687 TYR cc_start: 0.7688 (t80) cc_final: 0.7256 (t80) REVERT: F 798 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7957 (pt0) outliers start: 64 outliers final: 30 residues processed: 376 average time/residue: 0.1777 time to fit residues: 109.9083 Evaluate side-chains 318 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 chunk 226 optimal weight: 3.9990 chunk 301 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 120 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 GLN C 408 ASN C 467 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 49 GLN D 155 HIS ** D 288 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 = 0.4543 r_free = 0.4543 target = 0.160935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.114174 restraints weight = 71968.443| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.12 r_work: 0.3521 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33324 Z= 0.162 Angle : 0.557 10.687 45011 Z= 0.286 Chirality : 0.041 0.224 5107 Planarity : 0.004 0.060 5516 Dihedral : 11.788 176.302 4591 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.33 % Allowed : 18.19 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.70 (0.14), residues: 3852 helix: 0.44 (0.12), residues: 1887 sheet: -1.55 (0.29), residues: 389 loop : -1.19 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 389 TYR 0.036 0.001 TYR F 646 PHE 0.030 0.002 PHE D 324 TRP 0.018 0.001 TRP A 475 HIS 0.007 0.001 HIS E 499 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (33307) covalent geometry : angle 0.55714 / 0.29 (44977) SS BOND : bond 0.00330 / 0.21 ( 17) SS BOND : angle 0.77170 / 0.49 ( 34) hydrogen bonds : bond 0.03979 / 2.62 ( 1439) hydrogen bonds : angle 4.77924 / 3.40 ( 3948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 308 time to evaluate : 0.805 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 433 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7560 (t80) REVERT: A 434 MET cc_start: 0.7989 (mpp) cc_final: 0.7278 (mpp) REVERT: A 438 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8987 (pt) REVERT: A 471 LEU cc_start: 0.8947 (tp) cc_final: 0.8355 (pp) REVERT: A 501 LYS cc_start: 0.8822 (tttt) cc_final: 0.8481 (tptt) REVERT: A 694 HIS cc_start: 0.8123 (m170) cc_final: 0.7547 (m170) REVERT: B 232 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6276 (tp) REVERT: B 444 ASP cc_start: 0.8153 (m-30) cc_final: 0.7890 (t70) REVERT: C 265 MET cc_start: 0.7881 (tpp) cc_final: 0.7585 (tpt) REVERT: C 375 MET cc_start: 0.7260 (mtm) cc_final: 0.7044 (mtm) REVERT: C 379 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7813 (mm) REVERT: C 509 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7856 (Cg_exo) REVERT: C 549 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5903 (mt) REVERT: D 159 ILE cc_start: 0.9090 (tt) cc_final: 0.8833 (pt) REVERT: D 309 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: D 375 MET cc_start: 0.7826 (mtp) cc_final: 0.7533 (mtp) REVERT: E 29 ASP cc_start: 0.8383 (t0) cc_final: 0.7977 (m-30) REVERT: E 244 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8373 (t80) REVERT: E 263 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7736 (tp) REVERT: E 275 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8400 (t80) REVERT: E 394 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7817 (mt) REVERT: E 438 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8092 (tt) REVERT: E 477 TYR cc_start: 0.7731 (m-80) cc_final: 0.7519 (m-80) REVERT: E 499 HIS cc_start: 0.7214 (m170) cc_final: 0.6856 (m-70) REVERT: E 532 ASN cc_start: 0.5719 (m-40) cc_final: 0.5403 (m-40) REVERT: F 144 PHE cc_start: 0.7927 (t80) cc_final: 0.7607 (t80) REVERT: F 175 LEU cc_start: 0.8731 (tp) cc_final: 0.8515 (mt) REVERT: F 264 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: F 588 MET cc_start: 0.7587 (mmp) cc_final: 0.6865 (mmm) REVERT: F 687 TYR cc_start: 0.7877 (t80) cc_final: 0.7462 (t80) REVERT: F 735 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7333 (mtmm) outliers start: 84 outliers final: 39 residues processed: 378 average time/residue: 0.1850 time to fit residues: 113.2331 Evaluate side-chains 339 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 34 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 243 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 366 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 HIS ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS F 107 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.160167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.114083 restraints weight = 71239.048| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.01 r_work: 0.3518 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33324 Z= 0.182 Angle : 0.556 10.250 45011 Z= 0.286 Chirality : 0.041 0.181 5107 Planarity : 0.004 0.057 5516 Dihedral : 11.224 174.263 4591 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.05 % Allowed : 17.72 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.64 (0.14), residues: 3852 helix: 0.48 (0.12), residues: 1888 sheet: -1.65 (0.28), residues: 401 loop : -1.12 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 345 TYR 0.041 0.002 TYR F 646 PHE 0.026 0.002 PHE D 324 TRP 0.019 0.002 TRP F 509 HIS 0.006 0.001 HIS E 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (33307) covalent geometry : angle 0.55596 / 0.29 (44977) SS BOND : bond 0.00404 / 0.25 ( 17) SS BOND : angle 0.80650 / 0.52 ( 34) hydrogen bonds : bond 0.03877 / 2.55 ( 1439) hydrogen bonds : angle 4.66654 / 3.33 ( 3948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 306 time to evaluate : 1.091 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 433 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7450 (t80) REVERT: A 434 MET cc_start: 0.7963 (mpp) cc_final: 0.7216 (mpp) REVERT: A 438 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8884 (pt) REVERT: A 501 LYS cc_start: 0.8793 (tttt) cc_final: 0.8469 (tptt) REVERT: A 694 HIS cc_start: 0.8123 (m170) cc_final: 0.7598 (m170) REVERT: B 46 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7204 (tp40) REVERT: B 232 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6363 (tp) REVERT: B 239 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: B 377 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.7270 (m-70) REVERT: C 235 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8516 (tppp) REVERT: C 265 MET cc_start: 0.7880 (tpp) cc_final: 0.7563 (tpt) REVERT: C 375 MET cc_start: 0.7101 (mtm) cc_final: 0.6853 (mtm) REVERT: C 379 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 509 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7805 (Cg_exo) REVERT: D 159 ILE cc_start: 0.9069 (tt) cc_final: 0.8854 (pt) REVERT: D 244 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.5922 (m-80) REVERT: E 29 ASP cc_start: 0.8374 (t0) cc_final: 0.7940 (m-30) REVERT: E 244 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8357 (t80) REVERT: E 263 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7697 (tp) REVERT: E 275 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (t80) REVERT: E 394 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7927 (mt) REVERT: E 477 TYR cc_start: 0.7781 (m-80) cc_final: 0.7461 (m-80) REVERT: E 499 HIS cc_start: 0.7110 (m170) cc_final: 0.6673 (m-70) REVERT: F 144 PHE cc_start: 0.7970 (t80) cc_final: 0.7705 (t80) REVERT: F 175 LEU cc_start: 0.8848 (tp) cc_final: 0.8631 (mt) REVERT: F 503 MET cc_start: 0.7826 (mmm) cc_final: 0.7170 (tpp) REVERT: F 545 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6151 (tttm) REVERT: F 588 MET cc_start: 0.7385 (mmp) cc_final: 0.6766 (mmm) REVERT: F 687 TYR cc_start: 0.7876 (t80) cc_final: 0.7519 (t80) outliers start: 110 outliers final: 59 residues processed: 396 average time/residue: 0.1880 time to fit residues: 121.5296 Evaluate side-chains 353 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 282 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 438 ILE Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 201 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 HIS ** A 650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 755 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 ASN F 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.157876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.106341 restraints weight = 68995.123| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.35 r_work: 0.3465 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 33324 Z= 0.281 Angle : 0.613 8.398 45011 Z= 0.317 Chirality : 0.044 0.194 5107 Planarity : 0.004 0.063 5516 Dihedral : 11.039 167.579 4591 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.43 % Allowed : 18.24 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.80 (0.14), residues: 3852 helix: 0.35 (0.12), residues: 1881 sheet: -1.53 (0.28), residues: 400 loop : -1.24 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 346 TYR 0.020 0.002 TYR F 330 PHE 0.026 0.002 PHE B 353 TRP 0.032 0.002 TRP F 509 HIS 0.009 0.001 HIS E 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 (33307) covalent geometry : angle 0.61285 / 0.32 (44977) SS BOND : bond 0.00647 / 0.40 ( 17) SS BOND : angle 0.88816 / 0.57 ( 34) hydrogen bonds : bond 0.04235 / 2.78 ( 1439) hydrogen bonds : angle 4.77935 / 3.42 ( 3948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 293 time to evaluate : 1.102 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 433 PHE cc_start: 0.8214 (t80) cc_final: 0.7560 (t80) REVERT: A 434 MET cc_start: 0.8349 (mpp) cc_final: 0.7437 (mpp) REVERT: A 438 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8957 (pt) REVERT: A 471 LEU cc_start: 0.8958 (tp) cc_final: 0.8362 (pp) REVERT: A 501 LYS cc_start: 0.8856 (tttt) cc_final: 0.8516 (tptt) REVERT: A 694 HIS cc_start: 0.8192 (m170) cc_final: 0.7739 (m170) REVERT: B 46 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7401 (tp40) REVERT: B 232 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6891 (tp) REVERT: B 238 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7232 (tm-30) REVERT: B 239 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: B 434 MET cc_start: 0.6119 (mmt) cc_final: 0.5738 (mmt) REVERT: C 159 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 235 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8584 (tppp) REVERT: C 375 MET cc_start: 0.7546 (mtm) cc_final: 0.7314 (mtm) REVERT: C 379 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 413 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6083 (tp) REVERT: D 95 THR cc_start: 0.9078 (m) cc_final: 0.8851 (p) REVERT: D 155 HIS cc_start: 0.7613 (t-170) cc_final: 0.7393 (t-170) REVERT: D 159 ILE cc_start: 0.9089 (tt) cc_final: 0.8872 (pt) REVERT: D 244 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.5967 (m-80) REVERT: D 375 MET cc_start: 0.7928 (mtp) cc_final: 0.7681 (mtp) REVERT: E 29 ASP cc_start: 0.8553 (t0) cc_final: 0.8083 (m-30) REVERT: E 104 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8030 (t70) REVERT: E 233 ASP cc_start: 0.7610 (t0) cc_final: 0.7291 (t70) REVERT: E 244 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8456 (t80) REVERT: E 263 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7721 (tp) REVERT: E 394 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8127 (mt) REVERT: E 477 TYR cc_start: 0.7915 (m-80) cc_final: 0.7576 (m-80) REVERT: E 499 HIS cc_start: 0.7202 (m170) cc_final: 0.6871 (m-70) REVERT: E 660 ASN cc_start: 0.7911 (m-40) cc_final: 0.7446 (p0) REVERT: F 175 LEU cc_start: 0.8793 (tp) cc_final: 0.8572 (mt) REVERT: F 409 TRP cc_start: 0.6531 (m100) cc_final: 0.6186 (m100) REVERT: F 458 MET cc_start: 0.8318 (tpt) cc_final: 0.8064 (tpt) REVERT: F 503 MET cc_start: 0.7931 (mmm) cc_final: 0.7232 (tpp) REVERT: F 510 MET cc_start: 0.7884 (mmt) cc_final: 0.7634 (mmt) REVERT: F 545 LYS cc_start: 0.7559 (mmtt) cc_final: 0.6227 (tttm) REVERT: F 588 MET cc_start: 0.7605 (mmp) cc_final: 0.6985 (mmm) outliers start: 124 outliers final: 81 residues processed: 393 average time/residue: 0.1939 time to fit residues: 124.8256 Evaluate side-chains 380 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 287 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 453 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 147 optimal weight: 0.9990 chunk 367 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 295 optimal weight: 0.7980 chunk 290 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 306 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.159623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.111844 restraints weight = 68752.313| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.29 r_work: 0.3444 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33324 Z= 0.144 Angle : 0.538 10.131 45011 Z= 0.275 Chirality : 0.040 0.191 5107 Planarity : 0.004 0.068 5516 Dihedral : 10.204 159.710 4589 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.77 % Allowed : 19.02 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.57 (0.14), residues: 3852 helix: 0.57 (0.12), residues: 1873 sheet: -1.73 (0.27), residues: 429 loop : -1.06 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 345 TYR 0.030 0.001 TYR F 646 PHE 0.021 0.001 PHE D 324 TRP 0.060 0.002 TRP F 509 HIS 0.009 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (33307) covalent geometry : angle 0.53780 / 0.27 (44977) SS BOND : bond 0.00273 / 0.16 ( 17) SS BOND : angle 0.78160 / 0.50 ( 34) hydrogen bonds : bond 0.03675 / 2.41 ( 1439) hydrogen bonds : angle 4.52718 / 3.23 ( 3948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 1.190 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 433 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7364 (t80) REVERT: A 434 MET cc_start: 0.8237 (mpp) cc_final: 0.7151 (mpp) REVERT: A 471 LEU cc_start: 0.8883 (tp) cc_final: 0.8265 (pp) REVERT: A 501 LYS cc_start: 0.8824 (tttt) cc_final: 0.8493 (tptt) REVERT: A 597 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7287 (mp0) REVERT: A 623 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: A 694 HIS cc_start: 0.8250 (m170) cc_final: 0.7862 (m170) REVERT: A 708 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7206 (tp-100) REVERT: B 232 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6773 (tp) REVERT: B 239 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7909 (mp10) REVERT: B 375 MET cc_start: 0.6863 (mtm) cc_final: 0.6597 (mtm) REVERT: B 434 MET cc_start: 0.6025 (mmt) cc_final: 0.5664 (mmt) REVERT: C 235 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8545 (tppp) REVERT: C 265 MET cc_start: 0.7899 (tpp) cc_final: 0.7574 (tpt) REVERT: C 375 MET cc_start: 0.7347 (mtm) cc_final: 0.7127 (mtm) REVERT: C 379 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7897 (mm) REVERT: D 95 THR cc_start: 0.8999 (m) cc_final: 0.8770 (p) REVERT: D 159 ILE cc_start: 0.9130 (tt) cc_final: 0.8889 (pt) REVERT: D 244 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.5955 (m-80) REVERT: E 233 ASP cc_start: 0.7548 (t0) cc_final: 0.7245 (t70) REVERT: E 244 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8385 (t80) REVERT: E 263 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7593 (tp) REVERT: E 275 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8338 (t80) REVERT: E 477 TYR cc_start: 0.7945 (m-80) cc_final: 0.7650 (m-80) REVERT: E 499 HIS cc_start: 0.7120 (m170) cc_final: 0.6787 (m-70) REVERT: E 660 ASN cc_start: 0.7896 (m-40) cc_final: 0.7426 (p0) REVERT: F 175 LEU cc_start: 0.8741 (tp) cc_final: 0.8514 (mt) REVERT: F 458 MET cc_start: 0.8225 (tpt) cc_final: 0.7925 (tpt) REVERT: F 503 MET cc_start: 0.7872 (mmm) cc_final: 0.7236 (tpp) REVERT: F 510 MET cc_start: 0.7931 (mmt) cc_final: 0.7646 (mmt) REVERT: F 545 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6350 (tttm) REVERT: F 588 MET cc_start: 0.7532 (mmp) cc_final: 0.7145 (mmm) outliers start: 100 outliers final: 68 residues processed: 375 average time/residue: 0.1997 time to fit residues: 122.2927 Evaluate side-chains 362 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 284 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 715 CYS Chi-restraints excluded: chain F residue 784 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 324 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 364 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 758 GLN B 253 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 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 = 0.4486 r_free = 0.4486 target = 0.157193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106199 restraints weight = 68782.136| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.69 r_work: 0.3433 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 33324 Z= 0.303 Angle : 0.624 11.504 45011 Z= 0.322 Chirality : 0.044 0.143 5107 Planarity : 0.004 0.064 5516 Dihedral : 10.400 161.210 4589 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.38 % Allowed : 18.99 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.84 (0.14), residues: 3852 helix: 0.32 (0.12), residues: 1888 sheet: -1.52 (0.28), residues: 409 loop : -1.30 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 345 TYR 0.022 0.002 TYR F 511 PHE 0.025 0.002 PHE B 353 TRP 0.081 0.002 TRP F 509 HIS 0.009 0.001 HIS E 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.30 (33307) covalent geometry : angle 0.62344 / 0.32 (44977) SS BOND : bond 0.00652 / 0.39 ( 17) SS BOND : angle 0.87342 / 0.56 ( 34) hydrogen bonds : bond 0.04210 / 2.76 ( 1439) hydrogen bonds : angle 4.71059 / 3.37 ( 3948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 294 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 PHE cc_start: 0.8295 (t80) cc_final: 0.7639 (t80) REVERT: A 434 MET cc_start: 0.8450 (mpp) cc_final: 0.7345 (mpp) REVERT: A 471 LEU cc_start: 0.8993 (tp) cc_final: 0.8348 (pp) REVERT: A 501 LYS cc_start: 0.8898 (tttt) cc_final: 0.8543 (tptt) REVERT: A 623 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: A 694 HIS cc_start: 0.8323 (m170) cc_final: 0.7966 (m170) REVERT: A 708 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7308 (tp-100) REVERT: B 46 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7443 (tp40) REVERT: B 232 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.6883 (tp) REVERT: B 235 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8238 (mppt) REVERT: B 238 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 239 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: B 371 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7064 (t0) REVERT: B 434 MET cc_start: 0.6210 (mmt) cc_final: 0.5817 (mmt) REVERT: B 519 GLU cc_start: 0.7716 (tp30) cc_final: 0.7440 (tp30) REVERT: C 235 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8639 (tppp) REVERT: C 371 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7639 (t0) REVERT: C 375 MET cc_start: 0.7658 (mtm) cc_final: 0.7369 (mtm) REVERT: C 379 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7919 (mm) REVERT: D 95 THR cc_start: 0.9143 (m) cc_final: 0.8913 (p) REVERT: D 159 ILE cc_start: 0.9139 (tt) cc_final: 0.8890 (pt) REVERT: D 168 TRP cc_start: 0.7993 (t-100) cc_final: 0.7211 (t-100) REVERT: D 244 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: E 104 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.8121 (t70) REVERT: E 233 ASP cc_start: 0.7578 (t0) cc_final: 0.7244 (t70) REVERT: E 244 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8488 (t80) REVERT: E 263 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7661 (tp) REVERT: E 394 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8197 (mt) REVERT: E 477 TYR cc_start: 0.8060 (m-80) cc_final: 0.7745 (m-80) REVERT: E 499 HIS cc_start: 0.7161 (m170) cc_final: 0.6912 (m-70) REVERT: E 660 ASN cc_start: 0.8068 (m-40) cc_final: 0.7570 (p0) REVERT: F 175 LEU cc_start: 0.8748 (tp) cc_final: 0.8528 (mt) REVERT: F 510 MET cc_start: 0.8030 (mmt) cc_final: 0.7735 (mmt) REVERT: F 545 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6457 (tttm) REVERT: F 588 MET cc_start: 0.7662 (mmp) cc_final: 0.7179 (mmm) REVERT: F 615 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6918 (tp-100) outliers start: 122 outliers final: 83 residues processed: 400 average time/residue: 0.1957 time to fit residues: 128.2704 Evaluate side-chains 379 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 282 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 758 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 759 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 269 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 377 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 650 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.159516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.111738 restraints weight = 68978.003| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.10 r_work: 0.3460 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33324 Z= 0.128 Angle : 0.545 10.984 45011 Z= 0.277 Chirality : 0.040 0.187 5107 Planarity : 0.004 0.062 5516 Dihedral : 9.679 167.305 4589 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.52 % Allowed : 19.82 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.57 (0.14), residues: 3852 helix: 0.52 (0.12), residues: 1905 sheet: -1.29 (0.29), residues: 394 loop : -1.18 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 801 TYR 0.033 0.001 TYR F 646 PHE 0.019 0.001 PHE D 324 TRP 0.058 0.002 TRP F 509 HIS 0.008 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (33307) covalent geometry : angle 0.54473 / 0.28 (44977) SS BOND : bond 0.00235 / 0.15 ( 17) SS BOND : angle 0.76540 / 0.49 ( 34) hydrogen bonds : bond 0.03626 / 2.38 ( 1439) hydrogen bonds : angle 4.47606 / 3.20 ( 3948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 298 time to evaluate : 1.254 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 410 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: A 433 PHE cc_start: 0.8067 (t80) cc_final: 0.7433 (t80) REVERT: A 434 MET cc_start: 0.8308 (mpp) cc_final: 0.7384 (mpp) REVERT: A 471 LEU cc_start: 0.8905 (tp) cc_final: 0.8271 (pp) REVERT: A 501 LYS cc_start: 0.8792 (tttt) cc_final: 0.8425 (tptt) REVERT: A 557 LYS cc_start: 0.7928 (pttp) cc_final: 0.7544 (pptt) REVERT: A 597 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7267 (mp0) REVERT: A 694 HIS cc_start: 0.8313 (m170) cc_final: 0.7948 (m170) REVERT: A 708 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7213 (tp-100) REVERT: B 46 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7180 (tp40) REVERT: B 232 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6836 (tp) REVERT: B 235 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8255 (mppt) REVERT: B 238 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7129 (tm-30) REVERT: B 239 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: B 434 MET cc_start: 0.6066 (mmt) cc_final: 0.5679 (mmt) REVERT: C 234 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8724 (tptt) REVERT: C 265 MET cc_start: 0.7868 (tpp) cc_final: 0.7554 (tpt) REVERT: C 375 MET cc_start: 0.7246 (mtm) cc_final: 0.7008 (mtm) REVERT: C 379 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (mm) REVERT: D 49 GLN cc_start: 0.8778 (pm20) cc_final: 0.8047 (pm20) REVERT: D 95 THR cc_start: 0.9000 (m) cc_final: 0.8768 (p) REVERT: D 159 ILE cc_start: 0.9109 (tt) cc_final: 0.8860 (pt) REVERT: D 244 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: D 325 TYR cc_start: 0.8338 (t80) cc_final: 0.7913 (t80) REVERT: E 233 ASP cc_start: 0.7289 (t0) cc_final: 0.7086 (t70) REVERT: E 244 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8367 (t80) REVERT: E 263 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7628 (tp) REVERT: E 275 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8311 (t80) REVERT: E 477 TYR cc_start: 0.8041 (m-80) cc_final: 0.7740 (m-80) REVERT: E 499 HIS cc_start: 0.7077 (m170) cc_final: 0.6848 (m-70) REVERT: E 660 ASN cc_start: 0.8028 (m-40) cc_final: 0.7519 (p0) REVERT: F 175 LEU cc_start: 0.8606 (tp) cc_final: 0.8400 (mt) REVERT: F 510 MET cc_start: 0.8050 (mmt) cc_final: 0.7815 (mmt) REVERT: F 545 LYS cc_start: 0.7599 (mmtt) cc_final: 0.6587 (tttm) REVERT: F 546 ILE cc_start: 0.7268 (mt) cc_final: 0.6983 (mt) REVERT: F 588 MET cc_start: 0.7571 (mmp) cc_final: 0.7088 (mmm) REVERT: F 590 ASN cc_start: 0.8187 (m-40) cc_final: 0.7920 (m110) REVERT: F 615 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6920 (tp-100) outliers start: 91 outliers final: 66 residues processed: 373 average time/residue: 0.1850 time to fit residues: 112.2081 Evaluate side-chains 368 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 291 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 602 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 223 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 334 optimal weight: 0.6980 chunk 317 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN B 377 HIS ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.159723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.112875 restraints weight = 68559.025| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.34 r_work: 0.3451 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33324 Z= 0.128 Angle : 0.535 10.274 45011 Z= 0.271 Chirality : 0.040 0.289 5107 Planarity : 0.004 0.063 5516 Dihedral : 9.052 171.295 4589 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.38 % Allowed : 19.91 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.14), residues: 3852 helix: 0.65 (0.12), residues: 1903 sheet: -1.24 (0.29), residues: 399 loop : -1.13 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 801 TYR 0.026 0.001 TYR F 646 PHE 0.015 0.001 PHE D 324 TRP 0.049 0.002 TRP F 509 HIS 0.012 0.001 HIS E 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (33307) covalent geometry : angle 0.53496 / 0.27 (44977) SS BOND : bond 0.00279 / 0.17 ( 17) SS BOND : angle 0.76660 / 0.49 ( 34) hydrogen bonds : bond 0.03492 / 2.29 ( 1439) hydrogen bonds : angle 4.37272 / 3.13 ( 3948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 304 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8123 (pm20) REVERT: A 433 PHE cc_start: 0.7964 (t80) cc_final: 0.7284 (t80) REVERT: A 434 MET cc_start: 0.8305 (mpp) cc_final: 0.7343 (mpp) REVERT: A 468 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7618 (tp) REVERT: A 471 LEU cc_start: 0.8937 (tp) cc_final: 0.8162 (pp) REVERT: A 501 LYS cc_start: 0.8653 (tttt) cc_final: 0.8291 (tptt) REVERT: A 557 LYS cc_start: 0.7823 (pttp) cc_final: 0.7496 (pptt) REVERT: A 597 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7240 (mp0) REVERT: A 623 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: A 694 HIS cc_start: 0.8371 (m170) cc_final: 0.7991 (m170) REVERT: A 708 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7188 (tp-100) REVERT: B 46 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7219 (tp40) REVERT: B 115 GLU cc_start: 0.8270 (tp30) cc_final: 0.8025 (tp30) REVERT: B 232 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6874 (tp) REVERT: B 235 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8292 (mppt) REVERT: B 236 GLU cc_start: 0.8196 (tt0) cc_final: 0.7813 (tm-30) REVERT: B 238 GLU cc_start: 0.7529 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 239 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: B 434 MET cc_start: 0.6004 (mmt) cc_final: 0.5629 (mmt) REVERT: B 784 LEU cc_start: 0.3251 (OUTLIER) cc_final: 0.2609 (mt) REVERT: C 265 MET cc_start: 0.7785 (tpp) cc_final: 0.7471 (tpt) REVERT: D 49 GLN cc_start: 0.8750 (pm20) cc_final: 0.8026 (pm20) REVERT: D 95 THR cc_start: 0.8979 (m) cc_final: 0.8717 (p) REVERT: D 159 ILE cc_start: 0.9114 (tt) cc_final: 0.8856 (pt) REVERT: D 244 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: E 46 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7507 (tt0) REVERT: E 233 ASP cc_start: 0.7489 (t0) cc_final: 0.7204 (t70) REVERT: E 244 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8388 (t80) REVERT: E 263 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7540 (tp) REVERT: E 275 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8368 (t80) REVERT: E 477 TYR cc_start: 0.8032 (m-80) cc_final: 0.7732 (m-80) REVERT: E 660 ASN cc_start: 0.8077 (m-40) cc_final: 0.7549 (p0) REVERT: F 510 MET cc_start: 0.8087 (mmt) cc_final: 0.7877 (mmt) REVERT: F 545 LYS cc_start: 0.7654 (mmtt) cc_final: 0.6599 (tttm) REVERT: F 546 ILE cc_start: 0.7367 (mt) cc_final: 0.7099 (mt) REVERT: F 588 MET cc_start: 0.7636 (mmp) cc_final: 0.7171 (mmm) REVERT: F 590 ASN cc_start: 0.8119 (m-40) cc_final: 0.7855 (m110) REVERT: F 615 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6944 (tp-100) outliers start: 86 outliers final: 62 residues processed: 375 average time/residue: 0.2067 time to fit residues: 126.2044 Evaluate side-chains 368 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 293 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 PHE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 643 LYS Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 352 optimal weight: 9.9990 chunk 278 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 307 optimal weight: 0.9980 chunk 253 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS A 758 GLN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 606 HIS ** 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 = 0.4514 r_free = 0.4514 target = 0.159483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.113156 restraints weight = 68866.068| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.05 r_work: 0.3438 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33324 Z= 0.141 Angle : 0.554 11.221 45011 Z= 0.279 Chirality : 0.040 0.267 5107 Planarity : 0.004 0.061 5516 Dihedral : 8.794 172.697 4589 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.44 % Allowed : 20.16 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.14), residues: 3852 helix: 0.65 (0.12), residues: 1903 sheet: -1.20 (0.29), residues: 399 loop : -1.09 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.031 0.001 TYR F 646 PHE 0.017 0.001 PHE D 244 TRP 0.044 0.002 TRP F 509 HIS 0.011 0.001 HIS E 694 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (33307) covalent geometry : angle 0.55342 / 0.28 (44977) SS BOND : bond 0.00301 / 0.19 ( 17) SS BOND : angle 0.80511 / 0.51 ( 34) hydrogen bonds : bond 0.03489 / 2.28 ( 1439) hydrogen bonds : angle 4.37205 / 3.13 ( 3948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 300 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: A 433 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 434 MET cc_start: 0.8308 (mpp) cc_final: 0.7316 (mpp) REVERT: A 468 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7586 (tp) REVERT: A 471 LEU cc_start: 0.8951 (tp) cc_final: 0.8159 (pp) REVERT: A 501 LYS cc_start: 0.8622 (tttt) cc_final: 0.8277 (tptt) REVERT: A 557 LYS cc_start: 0.7773 (pttp) cc_final: 0.7450 (pptt) REVERT: A 597 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7262 (mp0) REVERT: A 623 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: A 694 HIS cc_start: 0.8398 (m170) cc_final: 0.8028 (m170) REVERT: A 708 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7184 (tp-100) REVERT: B 46 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7303 (tp40) REVERT: B 115 GLU cc_start: 0.8242 (tp30) cc_final: 0.8009 (tp30) REVERT: B 232 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.6887 (tp) REVERT: B 235 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8278 (mppt) REVERT: B 236 GLU cc_start: 0.8144 (tt0) cc_final: 0.7852 (tm-30) REVERT: B 238 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 239 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: B 434 MET cc_start: 0.6054 (mmt) cc_final: 0.5698 (mmt) REVERT: B 784 LEU cc_start: 0.3363 (OUTLIER) cc_final: 0.2671 (mt) REVERT: C 265 MET cc_start: 0.7853 (tpp) cc_final: 0.7563 (tpt) REVERT: D 49 GLN cc_start: 0.8740 (pm20) cc_final: 0.8042 (pm20) REVERT: D 95 THR cc_start: 0.8969 (m) cc_final: 0.8725 (p) REVERT: D 159 ILE cc_start: 0.9131 (tt) cc_final: 0.8869 (pt) REVERT: E 46 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7516 (tt0) REVERT: E 233 ASP cc_start: 0.7508 (t0) cc_final: 0.7247 (t70) REVERT: E 244 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8413 (t80) REVERT: E 263 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7634 (tp) REVERT: E 275 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8489 (t80) REVERT: E 477 TYR cc_start: 0.8059 (m-80) cc_final: 0.7762 (m-80) REVERT: E 660 ASN cc_start: 0.8135 (m-40) cc_final: 0.7617 (p0) REVERT: F 409 TRP cc_start: 0.6485 (m100) cc_final: 0.6086 (m100) REVERT: F 510 MET cc_start: 0.8101 (mmt) cc_final: 0.7843 (mmt) REVERT: F 545 LYS cc_start: 0.7612 (mmtt) cc_final: 0.6603 (tttm) REVERT: F 546 ILE cc_start: 0.7243 (mt) cc_final: 0.6977 (mt) REVERT: F 588 MET cc_start: 0.7627 (mmp) cc_final: 0.7167 (mmm) REVERT: F 590 ASN cc_start: 0.8153 (m-40) cc_final: 0.7882 (m110) REVERT: F 615 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6910 (tp-100) REVERT: F 643 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7846 (ptpp) outliers start: 88 outliers final: 65 residues processed: 372 average time/residue: 0.2035 time to fit residues: 123.3933 Evaluate side-chains 372 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 293 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 614 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 647 TRP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 666 ARG Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 THR Chi-restraints excluded: chain B residue 784 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 253 HIS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 483 ILE Chi-restraints excluded: chain E residue 541 ARG Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 692 LEU Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 176 SER Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 264 ARG Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 511 TYR Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 606 HIS Chi-restraints excluded: chain F residue 615 GLN Chi-restraints excluded: chain F residue 643 LYS Chi-restraints excluded: chain F residue 715 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 12 optimal weight: 0.9980 chunk 285 optimal weight: 0.0980 chunk 97 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 299 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 292 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 347 optimal weight: 0.1980 chunk 210 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 GLN ** C 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 606 HIS ** 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 = 0.4524 r_free = 0.4524 target = 0.160301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112228 restraints weight = 68830.388| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.24 r_work: 0.3461 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33324 Z= 0.112 Angle : 0.543 10.506 45011 Z= 0.274 Chirality : 0.040 0.282 5107 Planarity : 0.004 0.061 5516 Dihedral : 8.416 175.950 4589 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.16 % Allowed : 20.27 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.14), residues: 3852 helix: 0.68 (0.12), residues: 1908 sheet: -1.18 (0.29), residues: 398 loop : -1.04 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 419 TYR 0.031 0.001 TYR F 646 PHE 0.037 0.001 PHE E 324 TRP 0.041 0.002 TRP F 509 HIS 0.012 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (33307) covalent geometry : angle 0.54253 / 0.27 (44977) SS BOND : bond 0.00250 / 0.17 ( 17) SS BOND : angle 0.80752 / 0.50 ( 34) hydrogen bonds : bond 0.03379 / 2.21 ( 1439) hydrogen bonds : angle 4.33194 / 3.11 ( 3948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10823.71 seconds wall clock time: 185 minutes 26.65 seconds (11126.65 seconds total)