Starting phenix.real_space_refine on Tue Aug 26 10:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.map" model { file = "/net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rts_19495/08_2025/8rts_19495.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 234 5.16 5 C 23120 2.51 5 N 5802 2.21 5 O 6289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35445 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 5641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5641 Classifications: {'peptide': 692} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 667} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1599 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Time building chain proxies: 8.64, per 1000 atoms: 0.24 Number of scatterers: 35445 At special positions: 0 Unit cell: (160.146, 169.26, 201.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 234 16.00 O 6289 8.00 N 5802 7.00 C 23120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 308 " distance=2.02 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 308 " distance=2.02 Simple disulfide: pdb=" SG CYS C 115 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 308 " distance=2.02 Simple disulfide: pdb=" SG CYS D 115 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 308 " distance=2.02 Simple disulfide: pdb=" SG CYS E 115 " - pdb=" SG CYS E 293 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.02 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 308 " distance=2.02 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 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: 3.41 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8448 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 27 sheets defined 52.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 22 through 50 Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 121 through 148 Proline residue: A 128 - end of helix removed outlier: 4.691A pdb=" N TRP A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 4.112A pdb=" N LYS A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 4.088A pdb=" N THR A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.554A pdb=" N GLU A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 285 removed outlier: 4.334A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 341 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 381 through 390 removed outlier: 4.113A pdb=" N SER A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.543A pdb=" N VAL A 440 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.541A pdb=" N ILE A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 Processing helix chain 'A' and resid 507 through 513 removed outlier: 3.852A pdb=" N MET A 510 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 564 removed outlier: 4.350A pdb=" N VAL A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.631A pdb=" N HIS A 635 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 676 through 682 removed outlier: 3.710A pdb=" N CYS A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 722 through 728 removed outlier: 3.698A pdb=" N CYS A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'B' and resid 22 through 50 Processing helix chain 'B' and resid 104 through 119 Processing helix chain 'B' and resid 121 through 148 Proline residue: B 128 - end of helix removed outlier: 5.047A pdb=" N TRP B 145 " --> pdb=" O CYS B 141 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N PHE B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 148 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.752A pdb=" N LYS B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.865A pdb=" N THR B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.746A pdb=" N LEU B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 284 removed outlier: 3.714A pdb=" N ALA B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 312 through 341 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 381 through 390 removed outlier: 4.144A pdb=" N SER B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 409 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.656A pdb=" N LYS B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.600A pdb=" N ILE B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.556A pdb=" N ASP B 562 " --> pdb=" O GLN B 558 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 605 through 610 removed outlier: 4.468A pdb=" N PHE B 609 " --> pdb=" O PRO B 605 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 610 " --> pdb=" O HIS B 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 605 through 610' Processing helix chain 'B' and resid 629 through 636 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 677 through 682 removed outlier: 3.692A pdb=" N CYS B 682 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 722 through 728 Processing helix chain 'B' and resid 745 through 751 Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.618A pdb=" N LEU B 771 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 791 removed outlier: 3.528A pdb=" N THR B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 802 Processing helix chain 'C' and resid 22 through 50 Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 121 through 148 Proline residue: C 128 - end of helix removed outlier: 4.527A pdb=" N TRP C 145 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 removed outlier: 3.744A pdb=" N LYS C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 removed outlier: 4.269A pdb=" N THR C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 253 removed outlier: 3.860A pdb=" N LEU C 241 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 285 removed outlier: 3.793A pdb=" N ALA C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 343 removed outlier: 4.386A pdb=" N LEU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 367 through 381 Processing helix chain 'C' and resid 381 through 389 removed outlier: 4.034A pdb=" N SER C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 393 through 409 Processing helix chain 'C' and resid 410 through 418 Processing helix chain 'C' and resid 437 through 442 removed outlier: 3.609A pdb=" N PHE C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 482 through 493 Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.610A pdb=" N MET C 510 " --> pdb=" O PRO C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 606 through 611 Processing helix chain 'C' and resid 629 through 636 removed outlier: 3.688A pdb=" N HIS C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 676 through 682 removed outlier: 3.703A pdb=" N CYS C 682 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 722 through 728 Processing helix chain 'C' and resid 745 through 751 Processing helix chain 'C' and resid 768 through 774 removed outlier: 3.533A pdb=" N CYS C 774 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 791 Processing helix chain 'C' and resid 793 through 802 Processing helix chain 'D' and resid 22 through 50 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.553A pdb=" N LEU D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 148 Proline residue: D 128 - end of helix removed outlier: 4.592A pdb=" N TRP D 145 " --> pdb=" O CYS D 141 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N PHE D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 148 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 168 removed outlier: 3.578A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 237 through 252 removed outlier: 4.021A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 284 removed outlier: 4.231A pdb=" N ALA D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 343 Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 381 through 389 removed outlier: 4.108A pdb=" N SER D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 386 " --> pdb=" O PRO D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 393 through 409 Processing helix chain 'D' and resid 410 through 418 Processing helix chain 'D' and resid 437 through 443 removed outlier: 4.043A pdb=" N PHE D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 482 through 493 Processing helix chain 'D' and resid 507 through 513 removed outlier: 3.618A pdb=" N LEU D 513 " --> pdb=" O MET D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 629 through 634 removed outlier: 3.624A pdb=" N PHE D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 659 removed outlier: 3.533A pdb=" N ILE D 656 " --> pdb=" O PRO D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 682 removed outlier: 4.145A pdb=" N CYS D 682 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.731A pdb=" N CYS D 728 " --> pdb=" O LEU D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 751 Processing helix chain 'D' and resid 768 through 774 Processing helix chain 'D' and resid 785 through 791 Processing helix chain 'D' and resid 793 through 802 Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 121 through 148 removed outlier: 3.594A pdb=" N LYS E 125 " --> pdb=" O HIS E 121 " (cutoff:3.500A) Proline residue: E 128 - end of helix removed outlier: 4.240A pdb=" N TRP E 145 " --> pdb=" O CYS E 141 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE E 146 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 168 removed outlier: 4.354A pdb=" N LYS E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 4.222A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 253 removed outlier: 3.955A pdb=" N GLU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 284 removed outlier: 4.063A pdb=" N ALA E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 311 through 344 removed outlier: 4.173A pdb=" N LEU E 315 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 367 through 381 Processing helix chain 'E' and resid 381 through 389 removed outlier: 3.933A pdb=" N SER E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 392 No H-bonds generated for 'chain 'E' and resid 390 through 392' Processing helix chain 'E' and resid 393 through 409 Processing helix chain 'E' and resid 410 through 418 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 460 through 465 Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 507 through 513 removed outlier: 3.639A pdb=" N MET E 510 " --> pdb=" O PRO E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 563 Processing helix chain 'E' and resid 583 through 588 Processing helix chain 'E' and resid 607 through 611 Processing helix chain 'E' and resid 629 through 634 Processing helix chain 'E' and resid 653 through 659 Processing helix chain 'E' and resid 676 through 682 removed outlier: 3.876A pdb=" N CYS E 682 " --> pdb=" O LEU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 705 Processing helix chain 'E' and resid 722 through 728 removed outlier: 3.656A pdb=" N CYS E 728 " --> pdb=" O LEU E 725 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 751 Processing helix chain 'E' and resid 768 through 774 removed outlier: 3.502A pdb=" N LEU E 771 " --> pdb=" O PRO E 768 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 791 Processing helix chain 'E' and resid 793 through 802 Processing helix chain 'F' and resid 22 through 50 Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 148 Proline residue: F 128 - end of helix removed outlier: 4.268A pdb=" N TRP F 145 " --> pdb=" O CYS F 141 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 168 removed outlier: 4.146A pdb=" N LYS F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 removed outlier: 4.175A pdb=" N THR F 172 " --> pdb=" O SER F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 253 removed outlier: 3.762A pdb=" N LEU F 241 " --> pdb=" O GLN F 237 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 284 removed outlier: 4.055A pdb=" N ALA F 282 " --> pdb=" O ALA F 278 " (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 311 through 342 removed outlier: 4.825A pdb=" N LEU F 315 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 Processing helix chain 'F' and resid 367 through 381 Processing helix chain 'F' and resid 381 through 390 removed outlier: 3.536A pdb=" N SER F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL F 390 " --> pdb=" O LYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 409 Processing helix chain 'F' and resid 410 through 418 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 460 through 465 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 507 through 513 removed outlier: 4.167A pdb=" N MET F 510 " --> pdb=" O PRO F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 564 removed outlier: 4.180A pdb=" N VAL F 561 " --> pdb=" O PRO F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 582 through 588 Processing helix chain 'F' and resid 606 through 611 Processing helix chain 'F' and resid 629 through 635 removed outlier: 3.556A pdb=" N HIS F 635 " --> pdb=" O VAL F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.600A pdb=" N ILE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 682 removed outlier: 4.141A pdb=" N CYS F 682 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 705 Processing helix chain 'F' and resid 722 through 728 removed outlier: 3.701A pdb=" N CYS F 728 " --> pdb=" O LEU F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 745 through 751 Processing helix chain 'F' and resid 768 through 774 Processing helix chain 'F' and resid 785 through 791 Processing helix chain 'F' and resid 793 through 802 Processing helix chain 'G' and resid 22 through 50 Processing helix chain 'G' and resid 104 through 119 Processing helix chain 'G' and resid 121 through 148 Proline residue: G 128 - end of helix removed outlier: 4.569A pdb=" N TRP G 145 " --> pdb=" O CYS G 141 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 285 removed outlier: 4.156A pdb=" N ALA G 282 " --> pdb=" O ALA G 278 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 343 removed outlier: 3.554A pdb=" N CYS G 325 " --> pdb=" O PHE G 321 " (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 419 through 420 removed outlier: 5.767A pdb=" N LEU A 426 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LYS A 450 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 428 " --> pdb=" O LYS A 450 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLU A 452 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 449 " --> pdb=" O SER A 473 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N HIS A 475 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 451 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 472 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS A 499 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 474 " --> pdb=" O LYS A 499 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 496 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL A 522 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 498 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 547 " --> pdb=" O CYS A 571 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 573 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 549 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET A 570 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 597 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE A 572 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 618 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 459 removed outlier: 6.232A pdb=" N VAL A 457 " --> pdb=" O LYS A 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 710 through 712 removed outlier: 6.753A pdb=" N PHE A 711 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 757 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 removed outlier: 6.523A pdb=" N LEU B 430 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU B 451 " --> pdb=" O HIS B 475 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU B 474 " --> pdb=" O LYS B 499 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 519 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS B 550 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 521 " --> pdb=" O LYS B 550 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 595 " --> pdb=" O MET B 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 457 through 459 removed outlier: 6.229A pdb=" N VAL B 457 " --> pdb=" O LYS B 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 616 through 618 Processing sheet with id=AB1, first strand: chain 'B' and resid 710 through 712 removed outlier: 6.811A pdb=" N PHE B 711 " --> pdb=" O LYS B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 757 through 758 removed outlier: 6.841A pdb=" N LEU B 757 " --> pdb=" O VAL B 783 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 419 through 420 removed outlier: 5.958A pdb=" N LEU C 426 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS C 450 " --> pdb=" O LEU C 426 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 428 " --> pdb=" O LYS C 450 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU C 452 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 430 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU C 449 " --> pdb=" O SER C 473 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N HIS C 475 " --> pdb=" O LEU C 449 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 451 " --> pdb=" O HIS C 475 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU C 472 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS C 499 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU C 474 " --> pdb=" O LYS C 499 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 595 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 618 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 688 " --> pdb=" O SER C 712 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE C 711 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 757 " --> pdb=" O VAL C 783 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 457 through 459 removed outlier: 6.030A pdb=" N VAL C 457 " --> pdb=" O LYS C 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AB7, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AB8, first strand: chain 'D' and resid 429 through 430 removed outlier: 6.107A pdb=" N LEU D 430 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU D 449 " --> pdb=" O SER D 473 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS D 475 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU D 451 " --> pdb=" O HIS D 475 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU D 496 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL D 522 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL D 498 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 519 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS D 550 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 521 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU D 547 " --> pdb=" O CYS D 571 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N HIS D 573 " --> pdb=" O LEU D 547 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 549 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 595 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 597 " --> pdb=" O ILE D 572 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 688 " --> pdb=" O SER D 712 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N PHE D 711 " --> pdb=" O LYS D 735 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 734 " --> pdb=" O ASP D 758 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU D 757 " --> pdb=" O VAL D 783 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 457 through 458 removed outlier: 6.611A pdb=" N VAL D 457 " --> pdb=" O LYS D 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AC2, first strand: chain 'E' and resid 419 through 420 Processing sheet with id=AC3, first strand: chain 'E' and resid 429 through 430 removed outlier: 6.407A pdb=" N LEU E 430 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 451 " --> pdb=" O HIS E 475 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU E 474 " --> pdb=" O LYS E 499 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 519 " --> pdb=" O SER E 548 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LYS E 550 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU E 521 " --> pdb=" O LYS E 550 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 547 " --> pdb=" O CYS E 571 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N HIS E 573 " --> pdb=" O LEU E 547 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE E 549 " --> pdb=" O HIS E 573 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET E 570 " --> pdb=" O GLU E 593 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU E 595 " --> pdb=" O MET E 570 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 572 " --> pdb=" O GLU E 595 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 597 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU E 688 " --> pdb=" O SER E 712 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE E 711 " --> pdb=" O LYS E 735 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 757 " --> pdb=" O VAL E 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 457 through 459 removed outlier: 6.316A pdb=" N VAL E 457 " --> pdb=" O LYS E 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AC6, first strand: chain 'F' and resid 419 through 420 removed outlier: 5.577A pdb=" N LEU F 426 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS F 450 " --> pdb=" O LEU F 426 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU F 428 " --> pdb=" O LYS F 450 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU F 452 " --> pdb=" O LEU F 428 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU F 430 " --> pdb=" O GLU F 452 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU F 449 " --> pdb=" O SER F 473 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS F 475 " --> pdb=" O LEU F 449 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU F 451 " --> pdb=" O HIS F 475 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU F 472 " --> pdb=" O SER F 497 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS F 499 " --> pdb=" O LEU F 472 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU F 474 " --> pdb=" O LYS F 499 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU F 595 " --> pdb=" O MET F 570 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 572 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU F 642 " --> pdb=" O ARG F 664 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 457 through 459 removed outlier: 6.299A pdb=" N VAL F 457 " --> pdb=" O LYS F 480 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 710 through 712 removed outlier: 6.495A pdb=" N PHE F 711 " --> pdb=" O LYS F 735 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU F 757 " --> pdb=" O VAL F 783 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 52 through 56 1644 hydrogen bonds defined for protein. 4278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.22 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10978 1.34 - 1.46: 8173 1.46 - 1.58: 16721 1.58 - 1.70: 0 1.70 - 1.82: 357 Bond restraints: 36229 Sorted by residual: bond pdb=" N ILE E 649 " pdb=" CA ILE E 649 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.11e+01 bond pdb=" N PHE E 667 " pdb=" CA PHE E 667 " ideal model delta sigma weight residual 1.459 1.489 -0.030 9.10e-03 1.21e+04 1.06e+01 bond pdb=" N ILE B 766 " pdb=" CA ILE B 766 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N VAL F 759 " pdb=" CA VAL F 759 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.29e-02 6.01e+03 9.97e+00 bond pdb=" N ASN B 647 " pdb=" CA ASN B 647 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.15e-02 7.56e+03 9.90e+00 ... (remaining 36224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 48767 4.22 - 8.43: 178 8.43 - 12.65: 21 12.65 - 16.87: 0 16.87 - 21.09: 1 Bond angle restraints: 48967 Sorted by residual: angle pdb=" CA LEU C 36 " pdb=" CB LEU C 36 " pdb=" CG LEU C 36 " ideal model delta sigma weight residual 116.30 137.39 -21.09 3.50e+00 8.16e-02 3.63e+01 angle pdb=" C HIS B 527 " pdb=" CA HIS B 527 " pdb=" CB HIS B 527 " ideal model delta sigma weight residual 110.10 100.63 9.47 1.90e+00 2.77e-01 2.48e+01 angle pdb=" CA MET G 48 " pdb=" CB MET G 48 " pdb=" CG MET G 48 " ideal model delta sigma weight residual 114.10 123.92 -9.82 2.00e+00 2.50e-01 2.41e+01 angle pdb=" N GLU C 673 " pdb=" CA GLU C 673 " pdb=" C GLU C 673 " ideal model delta sigma weight residual 112.72 106.70 6.02 1.28e+00 6.10e-01 2.21e+01 angle pdb=" C TYR B 651 " pdb=" N ILE B 652 " pdb=" CA ILE B 652 " ideal model delta sigma weight residual 122.85 118.84 4.01 8.70e-01 1.32e+00 2.12e+01 ... (remaining 48962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 19703 17.02 - 34.03: 1778 34.03 - 51.05: 419 51.05 - 68.06: 55 68.06 - 85.08: 10 Dihedral angle restraints: 21965 sinusoidal: 9023 harmonic: 12942 Sorted by residual: dihedral pdb=" CD ARG B 531 " pdb=" NE ARG B 531 " pdb=" CZ ARG B 531 " pdb=" NH1 ARG B 531 " ideal model delta sinusoidal sigma weight residual 0.00 85.08 -85.08 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CD ARG E 531 " pdb=" NE ARG E 531 " pdb=" CZ ARG E 531 " pdb=" NH1 ARG E 531 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CD ARG D 531 " pdb=" NE ARG D 531 " pdb=" CZ ARG D 531 " pdb=" NH1 ARG D 531 " ideal model delta sinusoidal sigma weight residual 0.00 79.78 -79.78 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 21962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5206 0.086 - 0.172: 402 0.172 - 0.258: 20 0.258 - 0.343: 1 0.343 - 0.429: 1 Chirality restraints: 5630 Sorted by residual: chirality pdb=" CG LEU C 274 " pdb=" CB LEU C 274 " pdb=" CD1 LEU C 274 " pdb=" CD2 LEU C 274 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA MET G 48 " pdb=" N MET G 48 " pdb=" C MET G 48 " pdb=" CB MET G 48 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU B 274 " pdb=" CB LEU B 274 " pdb=" CD1 LEU B 274 " pdb=" CD2 LEU B 274 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 5627 not shown) Planarity restraints: 6029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 531 " -1.113 9.50e-02 1.11e+02 4.99e-01 1.50e+02 pdb=" NE ARG B 531 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 531 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 531 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 531 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 531 " 1.092 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG E 531 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG E 531 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 531 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 531 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 531 " 1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG D 531 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D 531 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 531 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 531 " 0.020 2.00e-02 2.50e+03 ... (remaining 6026 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 58 2.27 - 2.93: 16405 2.93 - 3.59: 57082 3.59 - 4.24: 88803 4.24 - 4.90: 144063 Nonbonded interactions: 306411 Sorted by model distance: nonbonded pdb=" O HIS C 763 " pdb=" OE2 GLU C 765 " model vdw 1.615 3.040 nonbonded pdb=" OE2 GLU B 673 " pdb=" OD2 ASP B 694 " model vdw 1.628 3.040 nonbonded pdb=" O SER F 742 " pdb=" OE1 GLU F 765 " model vdw 1.790 3.040 nonbonded pdb=" O HIS F 763 " pdb=" OE2 GLU F 765 " model vdw 1.830 3.040 nonbonded pdb=" OE1 GLU E 673 " pdb=" CG2 VAL E 674 " model vdw 1.831 3.460 ... (remaining 306406 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.370 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 0.058 36243 Z= 0.280 Angle : 0.749 21.087 48995 Z= 0.408 Chirality : 0.046 0.429 5630 Planarity : 0.014 0.499 6029 Dihedral : 13.520 85.081 13475 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 0.67 % Allowed : 18.41 % Favored : 80.92 % 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 aren not related in a simple way. whole: -0.52 (0.13), residues: 4290 helix: 0.04 (0.12), residues: 1946 sheet: -1.16 (0.22), residues: 622 loop : -0.24 (0.16), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 387 TYR 0.029 0.001 TYR B 279 PHE 0.032 0.001 PHE C 138 TRP 0.014 0.002 TRP C 170 HIS 0.011 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00502 (36229) covalent geometry : angle 0.74883 (48967) SS BOND : bond 0.00733 ( 14) SS BOND : angle 1.22687 ( 28) hydrogen bonds : bond 0.17179 ( 1644) hydrogen bonds : angle 6.96911 ( 4278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 667 PHE cc_start: 0.9674 (OUTLIER) cc_final: 0.9259 (m-80) REVERT: B 496 LEU cc_start: 0.9507 (tt) cc_final: 0.9300 (tp) REVERT: B 503 MET cc_start: 0.7828 (tpp) cc_final: 0.7189 (tpt) REVERT: C 570 MET cc_start: 0.4760 (ppp) cc_final: 0.4483 (ppp) REVERT: E 261 MET cc_start: 0.8619 (ppp) cc_final: 0.8365 (ppp) REVERT: E 376 MET cc_start: 0.9167 (ppp) cc_final: 0.8915 (ppp) REVERT: G 35 MET cc_start: -0.1248 (ttt) cc_final: -0.1605 (ttp) outliers start: 27 outliers final: 26 residues processed: 217 average time/residue: 0.2055 time to fit residues: 75.6459 Evaluate side-chains 222 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 531 ARG Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 531 ARG Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 666 SER Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 760 LYS Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 581 MET Chi-restraints excluded: chain F residue 759 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 0.1980 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 6.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 46 GLN ** D 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** 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 = 0.4439 r_free = 0.4439 target = 0.103535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.070459 restraints weight = 144436.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.067414 restraints weight = 99695.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.067480 restraints weight = 69435.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067255 restraints weight = 55120.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.067276 restraints weight = 54401.306| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 36243 Z= 0.253 Angle : 0.659 18.114 48995 Z= 0.339 Chirality : 0.042 0.281 5630 Planarity : 0.004 0.073 6029 Dihedral : 5.531 57.859 4702 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.13 % Allowed : 16.95 % Favored : 79.93 % 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 aren not related in a simple way. whole: -0.58 (0.13), residues: 4290 helix: 0.26 (0.12), residues: 2033 sheet: -1.36 (0.22), residues: 627 loop : -0.60 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 531 TYR 0.032 0.002 TYR B 279 PHE 0.017 0.001 PHE A 127 TRP 0.014 0.002 TRP B 509 HIS 0.008 0.001 HIS F 566 Details of bonding type rmsd covalent geometry : bond 0.00544 (36229) covalent geometry : angle 0.65848 (48967) SS BOND : bond 0.00881 ( 14) SS BOND : angle 1.32833 ( 28) hydrogen bonds : bond 0.05102 ( 1644) hydrogen bonds : angle 5.47462 ( 4278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 199 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9194 (mm) REVERT: B 540 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8946 (t0) REVERT: B 634 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: C 114 MET cc_start: 0.8993 (tpp) cc_final: 0.8641 (tpp) REVERT: C 274 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8602 (pp) REVERT: E 273 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8954 (t80) REVERT: E 373 MET cc_start: 0.9601 (ptp) cc_final: 0.9208 (ptp) REVERT: E 376 MET cc_start: 0.9193 (ppp) cc_final: 0.8986 (ppp) REVERT: F 261 MET cc_start: 0.8230 (ptm) cc_final: 0.7142 (mmm) REVERT: F 651 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7932 (t80) REVERT: G 35 MET cc_start: -0.1179 (ttt) cc_final: -0.1405 (ttp) outliers start: 126 outliers final: 64 residues processed: 307 average time/residue: 0.1890 time to fit residues: 98.6263 Evaluate side-chains 263 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 696 ARG Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 449 LEU Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 651 TYR Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 759 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 88 optimal weight: 0.9980 chunk 419 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 283 optimal weight: 2.9990 chunk 355 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 304 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 406 ASN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS C 706 GLN D 49 GLN ** D 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.105937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.072607 restraints weight = 139172.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.073346 restraints weight = 84417.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072277 restraints weight = 67025.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.072170 restraints weight = 65322.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.072147 restraints weight = 57997.695| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36243 Z= 0.128 Angle : 0.583 15.117 48995 Z= 0.293 Chirality : 0.041 0.261 5630 Planarity : 0.003 0.048 6029 Dihedral : 4.760 58.314 4660 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.03 % Allowed : 17.54 % Favored : 79.43 % 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 aren not related in a simple way. whole: -0.39 (0.13), residues: 4290 helix: 0.52 (0.12), residues: 2034 sheet: -1.41 (0.21), residues: 632 loop : -0.59 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.027 0.001 TYR B 279 PHE 0.025 0.001 PHE B 727 TRP 0.024 0.001 TRP C 645 HIS 0.031 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00274 (36229) covalent geometry : angle 0.58185 (48967) SS BOND : bond 0.00519 ( 14) SS BOND : angle 1.30073 ( 28) hydrogen bonds : bond 0.04150 ( 1644) hydrogen bonds : angle 4.95760 ( 4278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 202 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.9415 (ppp) cc_final: 0.8565 (tmm) REVERT: B 381 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8118 (p0) REVERT: B 432 MET cc_start: 0.8743 (mmm) cc_final: 0.8475 (mmm) REVERT: B 634 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: C 274 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 360 ILE cc_start: 0.1132 (OUTLIER) cc_final: 0.0909 (pt) REVERT: C 363 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5076 (mm) REVERT: D 314 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6900 (t70) REVERT: D 556 ILE cc_start: -0.0832 (OUTLIER) cc_final: -0.1119 (mm) REVERT: E 27 PHE cc_start: 0.8520 (m-80) cc_final: 0.8079 (m-80) REVERT: E 261 MET cc_start: 0.8598 (ppp) cc_final: 0.8345 (ppp) REVERT: E 273 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8869 (t80) REVERT: E 376 MET cc_start: 0.9118 (ppp) cc_final: 0.8913 (ppp) REVERT: F 117 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: F 261 MET cc_start: 0.8276 (ptm) cc_final: 0.7329 (mmm) REVERT: F 651 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7867 (t80) outliers start: 122 outliers final: 62 residues processed: 311 average time/residue: 0.1857 time to fit residues: 99.2014 Evaluate side-chains 269 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 197 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 651 TYR Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 759 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 316 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 404 optimal weight: 30.0000 chunk 16 optimal weight: 0.9980 chunk 170 optimal weight: 20.0000 chunk 271 optimal weight: 50.0000 chunk 158 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 ASN ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** 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 = 0.4433 r_free = 0.4433 target = 0.104831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.070822 restraints weight = 116119.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.071686 restraints weight = 89486.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.070476 restraints weight = 72002.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070525 restraints weight = 67216.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070551 restraints weight = 62935.199| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36243 Z= 0.238 Angle : 0.624 15.659 48995 Z= 0.317 Chirality : 0.042 0.283 5630 Planarity : 0.004 0.069 6029 Dihedral : 4.755 57.850 4656 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.92 % Allowed : 17.62 % Favored : 78.46 % 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 aren not related in a simple way. whole: -0.52 (0.13), residues: 4290 helix: 0.43 (0.12), residues: 2034 sheet: -1.49 (0.21), residues: 626 loop : -0.68 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 504 TYR 0.031 0.002 TYR B 279 PHE 0.017 0.001 PHE B 306 TRP 0.028 0.002 TRP B 145 HIS 0.014 0.001 HIS F 482 Details of bonding type rmsd covalent geometry : bond 0.00520 (36229) covalent geometry : angle 0.62343 (48967) SS BOND : bond 0.00870 ( 14) SS BOND : angle 1.28829 ( 28) hydrogen bonds : bond 0.04161 ( 1644) hydrogen bonds : angle 5.05422 ( 4278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 193 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 381 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8296 (p0) REVERT: B 540 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8963 (t0) REVERT: B 634 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: C 30 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: C 274 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8478 (pp) REVERT: C 363 ILE cc_start: 0.5117 (OUTLIER) cc_final: 0.4261 (mm) REVERT: C 367 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9008 (ptmm) REVERT: C 566 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7160 (p-80) REVERT: D 314 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7117 (t70) REVERT: D 556 ILE cc_start: -0.0692 (OUTLIER) cc_final: -0.1004 (mm) REVERT: D 655 HIS cc_start: 0.7215 (t-90) cc_final: 0.6953 (t-90) REVERT: E 27 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: E 37 MET cc_start: 0.9093 (mmt) cc_final: 0.8854 (mmt) REVERT: E 330 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: E 373 MET cc_start: 0.9561 (ptp) cc_final: 0.9228 (ptp) REVERT: F 261 MET cc_start: 0.8243 (ptm) cc_final: 0.7235 (mmm) REVERT: F 651 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7924 (t80) REVERT: G 135 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6034 (m) outliers start: 158 outliers final: 110 residues processed: 337 average time/residue: 0.1852 time to fit residues: 106.6802 Evaluate side-chains 314 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 190 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 473 SER Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 651 TYR Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain F residue 759 VAL Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 57 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 305 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 chunk 318 optimal weight: 10.0000 chunk 175 optimal weight: 0.1980 chunk 396 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 763 HIS ** G 134 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 = 0.4447 r_free = 0.4447 target = 0.104174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.068985 restraints weight = 142464.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.069035 restraints weight = 82683.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.068308 restraints weight = 56052.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.068316 restraints weight = 56438.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.068430 restraints weight = 50683.257| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36243 Z= 0.171 Angle : 0.587 14.744 48995 Z= 0.296 Chirality : 0.041 0.217 5630 Planarity : 0.003 0.060 6029 Dihedral : 4.666 58.044 4656 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.32 % Allowed : 18.16 % Favored : 77.52 % 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 aren not related in a simple way. whole: -0.44 (0.13), residues: 4290 helix: 0.49 (0.12), residues: 2030 sheet: -1.50 (0.21), residues: 632 loop : -0.62 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 637 TYR 0.030 0.001 TYR B 279 PHE 0.011 0.001 PHE B 306 TRP 0.016 0.001 TRP B 145 HIS 0.007 0.001 HIS E 475 Details of bonding type rmsd covalent geometry : bond 0.00377 (36229) covalent geometry : angle 0.58654 (48967) SS BOND : bond 0.00668 ( 14) SS BOND : angle 1.29914 ( 28) hydrogen bonds : bond 0.03930 ( 1644) hydrogen bonds : angle 4.88761 ( 4278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 198 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8621 (mt) REVERT: B 381 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8198 (p0) REVERT: B 588 MET cc_start: 0.7844 (mmp) cc_final: 0.7624 (mmp) REVERT: B 634 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6423 (pm20) REVERT: C 30 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: C 367 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.9023 (ptmm) REVERT: C 392 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7359 (tm) REVERT: C 566 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7167 (p-80) REVERT: D 314 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6983 (t70) REVERT: D 556 ILE cc_start: -0.0137 (OUTLIER) cc_final: -0.0497 (mm) REVERT: E 27 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: E 330 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: F 117 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: F 261 MET cc_start: 0.8217 (ptm) cc_final: 0.7220 (mmm) REVERT: F 342 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7248 (t80) REVERT: F 651 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.7974 (t80) outliers start: 174 outliers final: 113 residues processed: 355 average time/residue: 0.1907 time to fit residues: 115.4389 Evaluate side-chains 321 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 194 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 651 TYR Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 236 optimal weight: 30.0000 chunk 342 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 385 optimal weight: 6.9990 chunk 337 optimal weight: 20.0000 chunk 351 optimal weight: 0.5980 chunk 414 optimal weight: 40.0000 chunk 311 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 416 GLN E 280 ASN ** E 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** 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 = 0.4445 r_free = 0.4445 target = 0.103985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.069872 restraints weight = 142102.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.070939 restraints weight = 73496.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.069710 restraints weight = 57394.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.069878 restraints weight = 57376.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.069824 restraints weight = 52363.135| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36243 Z= 0.173 Angle : 0.598 13.693 48995 Z= 0.300 Chirality : 0.041 0.216 5630 Planarity : 0.003 0.063 6029 Dihedral : 4.636 58.609 4654 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.57 % Allowed : 18.41 % Favored : 77.02 % 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 aren not related in a simple way. whole: -0.46 (0.13), residues: 4290 helix: 0.50 (0.12), residues: 2040 sheet: -1.55 (0.21), residues: 636 loop : -0.63 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 504 TYR 0.030 0.001 TYR B 279 PHE 0.019 0.001 PHE F 242 TRP 0.034 0.002 TRP B 145 HIS 0.007 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00383 (36229) covalent geometry : angle 0.59781 (48967) SS BOND : bond 0.00679 ( 14) SS BOND : angle 1.26315 ( 28) hydrogen bonds : bond 0.03833 ( 1644) hydrogen bonds : angle 4.85260 ( 4278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 196 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 570 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: B 35 MET cc_start: 0.8983 (mtp) cc_final: 0.8552 (mtt) REVERT: B 381 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8215 (p0) REVERT: B 634 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: C 360 ILE cc_start: 0.1177 (OUTLIER) cc_final: 0.0963 (pt) REVERT: C 363 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.4972 (mm) REVERT: C 367 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9017 (ptmm) REVERT: C 392 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7440 (tm) REVERT: C 566 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7337 (p-80) REVERT: D 314 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7082 (t70) REVERT: D 556 ILE cc_start: -0.0456 (OUTLIER) cc_final: -0.0820 (mm) REVERT: E 27 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8093 (m-80) REVERT: E 330 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: E 373 MET cc_start: 0.9558 (ptp) cc_final: 0.9133 (ptp) REVERT: F 117 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: F 261 MET cc_start: 0.8201 (ptm) cc_final: 0.7273 (mmm) REVERT: F 342 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7224 (t80) REVERT: F 672 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (pt) REVERT: F 800 MET cc_start: 0.2303 (tpt) cc_final: 0.1666 (tpt) outliers start: 184 outliers final: 134 residues processed: 363 average time/residue: 0.1920 time to fit residues: 118.8077 Evaluate side-chains 343 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 193 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 279 TYR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 104 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 322 CYS Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 481 ILE Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 503 MET Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 672 ILE Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 299 ASP Chi-restraints excluded: chain G residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 26 optimal weight: 0.7980 chunk 269 optimal weight: 50.0000 chunk 216 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 207 optimal weight: 0.0570 chunk 279 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN C 49 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 HIS F 106 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** 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 = 0.4466 r_free = 0.4466 target = 0.105972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.071687 restraints weight = 138236.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.069443 restraints weight = 91630.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.069203 restraints weight = 70380.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.069131 restraints weight = 52432.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.069127 restraints weight = 50540.216| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 36243 Z= 0.110 Angle : 0.584 13.046 48995 Z= 0.288 Chirality : 0.040 0.248 5630 Planarity : 0.003 0.055 6029 Dihedral : 4.467 57.987 4652 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.42 % Allowed : 19.68 % Favored : 76.90 % 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 aren not related in a simple way. whole: -0.34 (0.13), residues: 4290 helix: 0.59 (0.12), residues: 2036 sheet: -1.40 (0.21), residues: 619 loop : -0.61 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 415 TYR 0.032 0.001 TYR B 323 PHE 0.022 0.001 PHE D 158 TRP 0.029 0.001 TRP B 145 HIS 0.006 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00237 (36229) covalent geometry : angle 0.58382 (48967) SS BOND : bond 0.00452 ( 14) SS BOND : angle 1.20690 ( 28) hydrogen bonds : bond 0.03605 ( 1644) hydrogen bonds : angle 4.64764 ( 4278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 207 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.7854 (tmm) REVERT: B 35 MET cc_start: 0.8943 (mtp) cc_final: 0.8674 (mtt) REVERT: B 48 MET cc_start: 0.8638 (mtp) cc_final: 0.8180 (ttm) REVERT: B 274 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (mm) REVERT: B 381 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8202 (p0) REVERT: B 598 HIS cc_start: 0.9132 (OUTLIER) cc_final: 0.8774 (t-170) REVERT: B 634 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6125 (pm20) REVERT: C 312 MET cc_start: 0.8180 (mmm) cc_final: 0.7945 (mmm) REVERT: C 360 ILE cc_start: 0.0941 (OUTLIER) cc_final: 0.0731 (pt) REVERT: C 363 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3509 (mm) REVERT: C 367 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8905 (ptmm) REVERT: C 392 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7700 (tm) REVERT: C 566 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6843 (p-80) REVERT: C 651 TYR cc_start: 0.7855 (p90) cc_final: 0.7622 (p90) REVERT: D 314 HIS cc_start: 0.7331 (OUTLIER) cc_final: 0.6929 (t70) REVERT: D 556 ILE cc_start: -0.0431 (OUTLIER) cc_final: -0.0773 (mm) REVERT: E 27 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: E 273 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8859 (t80) REVERT: E 373 MET cc_start: 0.9608 (ptp) cc_final: 0.9149 (ptp) REVERT: E 376 MET cc_start: 0.9159 (ppp) cc_final: 0.8923 (ppp) REVERT: F 117 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: F 261 MET cc_start: 0.8195 (ptm) cc_final: 0.7092 (mmm) REVERT: F 342 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7172 (t80) outliers start: 138 outliers final: 92 residues processed: 330 average time/residue: 0.1982 time to fit residues: 112.6216 Evaluate side-chains 302 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 194 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain E residue 634 GLN Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 390 VAL Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 299 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 352 optimal weight: 0.7980 chunk 370 optimal weight: 20.0000 chunk 187 optimal weight: 0.6980 chunk 424 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 425 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.104753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.070885 restraints weight = 139712.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.069154 restraints weight = 94862.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.068356 restraints weight = 63946.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.068394 restraints weight = 56023.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.068533 restraints weight = 50819.226| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36243 Z= 0.141 Angle : 0.591 15.296 48995 Z= 0.291 Chirality : 0.040 0.219 5630 Planarity : 0.003 0.062 6029 Dihedral : 4.444 56.526 4652 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.62 % Allowed : 19.80 % Favored : 76.58 % 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 aren not related in a simple way. whole: -0.37 (0.13), residues: 4290 helix: 0.58 (0.12), residues: 2043 sheet: -1.53 (0.21), residues: 629 loop : -0.60 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 514 TYR 0.036 0.001 TYR B 323 PHE 0.020 0.001 PHE D 158 TRP 0.017 0.001 TRP B 145 HIS 0.006 0.001 HIS E 475 Details of bonding type rmsd covalent geometry : bond 0.00311 (36229) covalent geometry : angle 0.59079 (48967) SS BOND : bond 0.00582 ( 14) SS BOND : angle 1.16620 ( 28) hydrogen bonds : bond 0.03559 ( 1644) hydrogen bonds : angle 4.68197 ( 4278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 197 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 570 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.7850 (tmm) REVERT: B 35 MET cc_start: 0.9019 (mtp) cc_final: 0.8620 (mtt) REVERT: B 274 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8593 (mm) REVERT: B 312 MET cc_start: 0.7723 (mtp) cc_final: 0.7462 (mtp) REVERT: B 381 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8269 (p0) REVERT: B 496 LEU cc_start: 0.9373 (tt) cc_final: 0.9107 (tp) REVERT: B 634 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: C 312 MET cc_start: 0.8062 (mmm) cc_final: 0.7835 (mmm) REVERT: C 360 ILE cc_start: 0.0950 (OUTLIER) cc_final: 0.0748 (pt) REVERT: C 363 ILE cc_start: 0.3373 (OUTLIER) cc_final: 0.2749 (mm) REVERT: C 367 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (ptmm) REVERT: C 392 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7759 (tm) REVERT: C 566 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6535 (p-80) REVERT: C 651 TYR cc_start: 0.7865 (p90) cc_final: 0.7636 (p90) REVERT: D 273 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (t80) REVERT: D 314 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.7060 (t70) REVERT: D 556 ILE cc_start: -0.0316 (OUTLIER) cc_final: -0.0625 (mm) REVERT: D 588 MET cc_start: 0.1951 (mmt) cc_final: 0.1488 (mmm) REVERT: E 27 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: E 273 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8862 (t80) REVERT: E 376 MET cc_start: 0.9203 (ppp) cc_final: 0.8985 (ppp) REVERT: F 117 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: F 261 MET cc_start: 0.8214 (ptm) cc_final: 0.7127 (mmm) REVERT: F 342 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7240 (t80) outliers start: 146 outliers final: 106 residues processed: 329 average time/residue: 0.1890 time to fit residues: 107.5293 Evaluate side-chains 317 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 194 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 566 HIS Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 299 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 254 optimal weight: 50.0000 chunk 92 optimal weight: 0.0270 chunk 308 optimal weight: 0.9990 chunk 288 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 ASN ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.104033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3813 r_free = 0.3813 target = 0.069440 restraints weight = 121336.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.069899 restraints weight = 67183.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.069729 restraints weight = 49390.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.069744 restraints weight = 55462.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.069732 restraints weight = 47224.545| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36243 Z= 0.134 Angle : 0.603 15.112 48995 Z= 0.295 Chirality : 0.041 0.255 5630 Planarity : 0.003 0.058 6029 Dihedral : 4.421 56.369 4651 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.50 % Allowed : 20.07 % Favored : 76.43 % 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 aren not related in a simple way. whole: -0.39 (0.13), residues: 4290 helix: 0.55 (0.12), residues: 2052 sheet: -1.54 (0.21), residues: 629 loop : -0.60 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 514 TYR 0.039 0.001 TYR B 323 PHE 0.017 0.001 PHE D 158 TRP 0.029 0.002 TRP D 145 HIS 0.006 0.001 HIS D 655 Details of bonding type rmsd covalent geometry : bond 0.00297 (36229) covalent geometry : angle 0.60258 (48967) SS BOND : bond 0.00565 ( 14) SS BOND : angle 1.17479 ( 28) hydrogen bonds : bond 0.03538 ( 1644) hydrogen bonds : angle 4.64878 ( 4278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 198 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8546 (mt) REVERT: A 570 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.7723 (tmm) REVERT: B 35 MET cc_start: 0.8933 (mtp) cc_final: 0.8615 (mtt) REVERT: B 274 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8500 (mm) REVERT: B 381 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8266 (p0) REVERT: B 496 LEU cc_start: 0.9545 (tt) cc_final: 0.9038 (mt) REVERT: B 634 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: C 114 MET cc_start: 0.8956 (tpp) cc_final: 0.8442 (tpp) REVERT: C 312 MET cc_start: 0.8243 (mmm) cc_final: 0.7999 (mmm) REVERT: C 367 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8924 (ptmm) REVERT: C 566 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6357 (p-80) REVERT: D 273 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8793 (t80) REVERT: D 314 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.7035 (t70) REVERT: D 556 ILE cc_start: -0.0355 (OUTLIER) cc_final: -0.0634 (mm) REVERT: E 27 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: E 273 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8837 (t80) REVERT: E 376 MET cc_start: 0.9144 (ppp) cc_final: 0.8918 (ppp) REVERT: F 117 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: F 261 MET cc_start: 0.8184 (ptm) cc_final: 0.7033 (mmm) REVERT: F 342 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7142 (t80) REVERT: F 540 ASP cc_start: 0.9478 (OUTLIER) cc_final: 0.9190 (t0) outliers start: 141 outliers final: 106 residues processed: 325 average time/residue: 0.2023 time to fit residues: 112.9125 Evaluate side-chains 314 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 193 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 763 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 598 HIS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 273 PHE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 299 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 318 optimal weight: 30.0000 chunk 115 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 247 optimal weight: 50.0000 chunk 189 optimal weight: 20.0000 chunk 350 optimal weight: 0.7980 chunk 151 optimal weight: 20.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 763 HIS ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 763 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.104382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.070950 restraints weight = 120592.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.072320 restraints weight = 66839.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.071395 restraints weight = 47819.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.071376 restraints weight = 49923.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.071688 restraints weight = 47318.011| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36243 Z= 0.118 Angle : 0.608 14.924 48995 Z= 0.294 Chirality : 0.040 0.257 5630 Planarity : 0.003 0.059 6029 Dihedral : 4.369 55.882 4651 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.03 % Allowed : 20.50 % Favored : 76.48 % 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 aren not related in a simple way. whole: -0.30 (0.13), residues: 4290 helix: 0.64 (0.12), residues: 2028 sheet: -1.57 (0.21), residues: 634 loop : -0.50 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 514 TYR 0.042 0.001 TYR B 323 PHE 0.016 0.001 PHE D 158 TRP 0.017 0.001 TRP D 145 HIS 0.005 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00259 (36229) covalent geometry : angle 0.60783 (48967) SS BOND : bond 0.00510 ( 14) SS BOND : angle 1.13190 ( 28) hydrogen bonds : bond 0.03492 ( 1644) hydrogen bonds : angle 4.58225 ( 4278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8580 Ramachandran restraints generated. 4290 Oldfield, 0 Emsley, 4290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 199 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 261 MET cc_start: 0.7853 (mmm) cc_final: 0.7601 (mtt) REVERT: A 570 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7719 (tmm) REVERT: B 35 MET cc_start: 0.9181 (mtp) cc_final: 0.8711 (mtt) REVERT: B 274 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8588 (mm) REVERT: B 381 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8251 (p0) REVERT: B 496 LEU cc_start: 0.9493 (tt) cc_final: 0.9080 (mt) REVERT: B 588 MET cc_start: 0.7261 (mmp) cc_final: 0.7027 (mmp) REVERT: C 312 MET cc_start: 0.8168 (mmm) cc_final: 0.7947 (mmm) REVERT: C 367 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8942 (ptmm) REVERT: C 566 HIS cc_start: 0.6719 (OUTLIER) cc_final: 0.6266 (p-80) REVERT: D 314 HIS cc_start: 0.7292 (OUTLIER) cc_final: 0.7016 (t70) REVERT: D 556 ILE cc_start: -0.0391 (OUTLIER) cc_final: -0.0666 (mm) REVERT: E 27 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: E 376 MET cc_start: 0.9157 (ppp) cc_final: 0.8934 (ppp) REVERT: F 117 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: F 261 MET cc_start: 0.8190 (ptm) cc_final: 0.7035 (mmm) REVERT: F 342 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7197 (t80) outliers start: 122 outliers final: 102 residues processed: 309 average time/residue: 0.1876 time to fit residues: 100.0361 Evaluate side-chains 311 residues out of total 4072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 198 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 775 ARG Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 598 HIS Chi-restraints excluded: chain B residue 635 HIS Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 566 HIS Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 556 ILE Chi-restraints excluded: chain D residue 598 HIS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain E residue 27 PHE Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 96 MET Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 330 TYR Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain E residue 704 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 342 PHE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 580 VAL Chi-restraints excluded: chain F residue 598 HIS Chi-restraints excluded: chain F residue 704 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain G residue 299 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 337 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 420 optimal weight: 0.9990 chunk 294 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 375 HIS ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 635 HIS F 763 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.106016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.073161 restraints weight = 133517.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.073904 restraints weight = 83304.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.072648 restraints weight = 66531.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.072730 restraints weight = 60142.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.072717 restraints weight = 56532.632| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36243 Z= 0.105 Angle : 0.614 13.912 48995 Z= 0.294 Chirality : 0.041 0.256 5630 Planarity : 0.003 0.056 6029 Dihedral : 4.292 55.692 4651 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.73 % Allowed : 20.89 % Favored : 76.38 % 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 aren not related in a simple way. whole: -0.28 (0.13), residues: 4290 helix: 0.64 (0.12), residues: 2042 sheet: -1.53 (0.21), residues: 630 loop : -0.51 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 514 TYR 0.038 0.001 TYR B 323 PHE 0.014 0.001 PHE D 158 TRP 0.018 0.001 TRP D 145 HIS 0.006 0.001 HIS C 598 Details of bonding type rmsd covalent geometry : bond 0.00224 (36229) covalent geometry : angle 0.61376 (48967) SS BOND : bond 0.00463 ( 14) SS BOND : angle 1.09106 ( 28) hydrogen bonds : bond 0.03402 ( 1644) hydrogen bonds : angle 4.50814 ( 4278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11018.55 seconds wall clock time: 189 minutes 15.95 seconds (11355.95 seconds total)