Starting phenix.real_space_refine on Tue Jan 14 18:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.map" model { file = "/net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yka_39360/01_2025/8yka_39360.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.075 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 261 5.16 5 C 31122 2.51 5 N 8739 2.21 5 O 9264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 259 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 49386 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "B" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "E" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "F" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "C" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "D" Number of atoms: 6002 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} Conformer: "B" Number of residues, atoms: 764, 5994 Classifications: {'peptide': 764} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 721} bond proxies already assigned to first conformer: 6084 Chain: "2" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4458 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 29, 'TRANS': 539} Chain: "3" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4458 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 29, 'TRANS': 539} Chain: "1" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4458 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 29, 'TRANS': 539} Time building chain proxies: 31.68, per 1000 atoms: 0.64 Number of scatterers: 49386 At special positions: 0 Unit cell: (187.45, 190.682, 183.141, 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 261 16.00 O 9264 8.00 N 8739 7.00 C 31122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.72 Conformation dependent library (CDL) restraints added in 7.9 seconds 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11688 Finding SS restraints... Secondary structure from input PDB file: 291 helices and 58 sheets defined 42.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.749A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 190 through 198 removed outlier: 3.875A pdb=" N GLU A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.846A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.655A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.371A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.653A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.720A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.950A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 425 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.759A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 removed outlier: 4.003A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 4.235A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.562A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 4.350A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 removed outlier: 3.516A pdb=" N GLN A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 600 through 610 Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.515A pdb=" N ASN A 616 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.938A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 714 removed outlier: 3.584A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 752 through 763 removed outlier: 3.753A pdb=" N PHE A 758 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 4.572A pdb=" N LEU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 4.246A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 129 through 140 removed outlier: 4.271A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 190 through 192 No H-bonds generated for 'chain 'B' and resid 190 through 192' Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.962A pdb=" N SER B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 4.150A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix removed outlier: 3.580A pdb=" N HIS B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.872A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.565A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.999A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.947A pdb=" N SER B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.617A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.850A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.927A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 438 through 444 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 480 removed outlier: 4.364A pdb=" N ILE B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 480 " --> pdb=" O TRP B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 480' Processing helix chain 'B' and resid 482 through 494 removed outlier: 4.445A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 501 through 506 Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.197A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.992A pdb=" N THR B 549 " --> pdb=" O PRO B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 600 through 610 Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.598A pdb=" N ASN B 616 " --> pdb=" O THR B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.761A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.795A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 716 removed outlier: 3.888A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 692 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 720 removed outlier: 3.648A pdb=" N MET B 720 " --> pdb=" O PRO B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 720' Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 755 through 763 removed outlier: 3.757A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 18 removed outlier: 4.372A pdb=" N LEU E 17 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 18 " --> pdb=" O ALA E 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 14 through 18' Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.830A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 192 through 198 removed outlier: 3.541A pdb=" N GLU E 196 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 220 removed outlier: 3.659A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 3.884A pdb=" N ARG E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 221 through 226' Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.862A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.656A pdb=" N ILE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 removed outlier: 4.205A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 297 removed outlier: 4.262A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU E 294 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.805A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 4.000A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 425 Processing helix chain 'E' and resid 438 through 444 removed outlier: 3.939A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 484 through 491 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 525 through 535 removed outlier: 3.611A pdb=" N ILE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 4.584A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 568 removed outlier: 3.527A pdb=" N PHE E 563 " --> pdb=" O VAL E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 600 through 610 Processing helix chain 'E' and resid 612 through 616 removed outlier: 3.519A pdb=" N ASN E 616 " --> pdb=" O THR E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 661 removed outlier: 3.571A pdb=" N LYS E 658 " --> pdb=" O VAL E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 4.188A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 714 removed outlier: 3.846A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 740 Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 752 through 763 removed outlier: 3.542A pdb=" N PHE E 758 " --> pdb=" O LYS E 754 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR E 761 " --> pdb=" O MET E 757 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 49 removed outlier: 4.629A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 removed outlier: 4.304A pdb=" N ARG F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.537A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 192 No H-bonds generated for 'chain 'F' and resid 190 through 192' Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.769A pdb=" N SER F 197 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.503A pdb=" N HIS F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.796A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.885A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 removed outlier: 3.769A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.973A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.927A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 322 through 334 removed outlier: 3.882A pdb=" N SER F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 331 " --> pdb=" O GLN F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.684A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 358 Processing helix chain 'F' and resid 375 through 385 removed outlier: 3.867A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.069A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 427 removed outlier: 3.515A pdb=" N CYS F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.514A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 457 " --> pdb=" O ARG F 453 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 480 removed outlier: 4.291A pdb=" N ILE F 479 " --> pdb=" O THR F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 494 removed outlier: 4.681A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 501 through 506 removed outlier: 3.567A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.500A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR F 549 " --> pdb=" O PRO F 545 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 568 removed outlier: 3.648A pdb=" N GLN F 568 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 600 through 610 Processing helix chain 'F' and resid 612 through 616 removed outlier: 3.642A pdb=" N ASN F 616 " --> pdb=" O THR F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.663A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 4.174A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 716 removed outlier: 3.850A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 692 " --> pdb=" O THR F 688 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 697 " --> pdb=" O ARG F 693 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA F 698 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 705 " --> pdb=" O GLU F 701 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 710 " --> pdb=" O GLU F 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 720 removed outlier: 3.631A pdb=" N MET F 720 " --> pdb=" O PRO F 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 717 through 720' Processing helix chain 'F' and resid 735 through 740 Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 752 Processing helix chain 'F' and resid 755 through 763 removed outlier: 3.664A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR F 761 " --> pdb=" O MET F 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 4.447A pdb=" N LEU C 17 " --> pdb=" O THR C 14 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C 18 " --> pdb=" O ALA C 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 14 through 18' Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.835A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.817A pdb=" N GLU C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.592A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.784A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 234 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 removed outlier: 3.697A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 removed outlier: 4.432A pdb=" N MET C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 297 removed outlier: 4.293A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 4.090A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.631A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 385 removed outlier: 3.661A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.146A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 417 Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.820A pdb=" N GLN C 421 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE C 423 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 3.526A pdb=" N SER C 457 " --> pdb=" O ARG C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 484 through 494 removed outlier: 4.436A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.180A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 removed outlier: 3.571A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.742A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 568 removed outlier: 3.587A pdb=" N GLN C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 585 Processing helix chain 'C' and resid 600 through 610 Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.512A pdb=" N ASN C 616 " --> pdb=" O THR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.572A pdb=" N LYS C 658 " --> pdb=" O VAL C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 4.092A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 714 removed outlier: 3.819A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 752 through 763 removed outlier: 3.780A pdb=" N PHE C 758 " --> pdb=" O LYS C 754 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C 761 " --> pdb=" O MET C 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 removed outlier: 4.600A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.658A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 removed outlier: 3.647A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.771A pdb=" N SER D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 removed outlier: 3.652A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.936A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.697A pdb=" N ARG D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.769A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.996A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 334 removed outlier: 3.652A pdb=" N ILE D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 373 through 385 removed outlier: 4.196A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.915A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 427 removed outlier: 3.734A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.516A pdb=" N SER D 457 " --> pdb=" O ARG D 453 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 458 " --> pdb=" O TRP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 removed outlier: 4.880A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.513A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 535 Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.983A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 551 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 568 removed outlier: 3.518A pdb=" N PHE D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 600 through 610 Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.598A pdb=" N ASN D 616 " --> pdb=" O THR D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 removed outlier: 3.769A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.907A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 716 removed outlier: 3.698A pdb=" N LEU D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 720 Processing helix chain 'D' and resid 735 through 740 Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 752 Processing helix chain 'D' and resid 755 through 763 removed outlier: 3.585A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 129 Processing helix chain '2' and resid 130 through 135 Processing helix chain '2' and resid 159 through 166 removed outlier: 3.567A pdb=" N LEU 2 162 " --> pdb=" O ASP 2 159 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP 2 165 " --> pdb=" O LEU 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 175 Processing helix chain '2' and resid 186 through 191 Processing helix chain '2' and resid 191 through 202 removed outlier: 4.050A pdb=" N ASP 2 197 " --> pdb=" O ASP 2 193 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 2 200 " --> pdb=" O GLU 2 196 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN 2 202 " --> pdb=" O ILE 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 229 Processing helix chain '2' and resid 234 through 249 removed outlier: 3.658A pdb=" N LEU 2 238 " --> pdb=" O PHE 2 234 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG 2 239 " --> pdb=" O TRP 2 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 2 240 " --> pdb=" O HIS 2 236 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU 2 242 " --> pdb=" O LEU 2 238 " (cutoff:3.500A) Processing helix chain '2' and resid 249 through 258 removed outlier: 3.585A pdb=" N LEU 2 256 " --> pdb=" O ARG 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 262 through 273 removed outlier: 3.572A pdb=" N TRP 2 266 " --> pdb=" O ASP 2 262 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU 2 267 " --> pdb=" O ALA 2 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS 2 273 " --> pdb=" O ILE 2 269 " (cutoff:3.500A) Processing helix chain '2' and resid 289 through 299 Processing helix chain '2' and resid 308 through 314 Processing helix chain '2' and resid 328 through 333 removed outlier: 3.985A pdb=" N THR 2 333 " --> pdb=" O GLU 2 330 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 389 removed outlier: 3.724A pdb=" N LYS 2 387 " --> pdb=" O ASP 2 383 " (cutoff:3.500A) Processing helix chain '2' and resid 406 through 426 removed outlier: 3.831A pdb=" N LEU 2 410 " --> pdb=" O GLN 2 406 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 2 412 " --> pdb=" O LYS 2 408 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL 2 420 " --> pdb=" O ALA 2 416 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP 2 423 " --> pdb=" O GLU 2 419 " (cutoff:3.500A) Processing helix chain '2' and resid 428 through 439 Processing helix chain '2' and resid 440 through 444 Processing helix chain '2' and resid 449 through 463 removed outlier: 3.587A pdb=" N VAL 2 453 " --> pdb=" O GLN 2 449 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 2 458 " --> pdb=" O THR 2 454 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS 2 459 " --> pdb=" O ALA 2 455 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA 2 460 " --> pdb=" O ALA 2 456 " (cutoff:3.500A) Processing helix chain '2' and resid 481 through 485 Processing helix chain '2' and resid 489 through 500 removed outlier: 3.629A pdb=" N ALA 2 495 " --> pdb=" O LEU 2 491 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS 2 496 " --> pdb=" O TYR 2 492 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER 2 497 " --> pdb=" O ASN 2 493 " (cutoff:3.500A) Processing helix chain '2' and resid 615 through 619 Processing helix chain '2' and resid 621 through 634 removed outlier: 3.983A pdb=" N MET 2 627 " --> pdb=" O TYR 2 623 " (cutoff:3.500A) Processing helix chain '2' and resid 639 through 656 removed outlier: 4.059A pdb=" N LEU 2 643 " --> pdb=" O GLY 2 639 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR 2 650 " --> pdb=" O LYS 2 646 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS 2 653 " --> pdb=" O HIS 2 649 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 129 Processing helix chain '3' and resid 130 through 135 Processing helix chain '3' and resid 159 through 166 removed outlier: 3.567A pdb=" N LEU 3 162 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP 3 165 " --> pdb=" O LEU 3 162 " (cutoff:3.500A) Processing helix chain '3' and resid 171 through 175 Processing helix chain '3' and resid 186 through 191 Processing helix chain '3' and resid 191 through 202 removed outlier: 4.051A pdb=" N ASP 3 197 " --> pdb=" O ASP 3 193 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 3 200 " --> pdb=" O GLU 3 196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN 3 202 " --> pdb=" O ILE 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 218 through 229 Processing helix chain '3' and resid 234 through 249 removed outlier: 3.658A pdb=" N LEU 3 238 " --> pdb=" O PHE 3 234 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG 3 239 " --> pdb=" O TRP 3 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 3 240 " --> pdb=" O HIS 3 236 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU 3 242 " --> pdb=" O LEU 3 238 " (cutoff:3.500A) Processing helix chain '3' and resid 249 through 258 removed outlier: 3.584A pdb=" N LEU 3 256 " --> pdb=" O ARG 3 252 " (cutoff:3.500A) Processing helix chain '3' and resid 262 through 273 removed outlier: 3.572A pdb=" N TRP 3 266 " --> pdb=" O ASP 3 262 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU 3 267 " --> pdb=" O ALA 3 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 3 268 " --> pdb=" O ALA 3 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS 3 273 " --> pdb=" O ILE 3 269 " (cutoff:3.500A) Processing helix chain '3' and resid 289 through 299 Processing helix chain '3' and resid 308 through 314 Processing helix chain '3' and resid 328 through 333 removed outlier: 3.985A pdb=" N THR 3 333 " --> pdb=" O GLU 3 330 " (cutoff:3.500A) Processing helix chain '3' and resid 383 through 389 removed outlier: 3.725A pdb=" N LYS 3 387 " --> pdb=" O ASP 3 383 " (cutoff:3.500A) Processing helix chain '3' and resid 406 through 426 removed outlier: 3.831A pdb=" N LEU 3 410 " --> pdb=" O GLN 3 406 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 3 412 " --> pdb=" O LYS 3 408 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL 3 420 " --> pdb=" O ALA 3 416 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP 3 423 " --> pdb=" O GLU 3 419 " (cutoff:3.500A) Processing helix chain '3' and resid 428 through 439 Processing helix chain '3' and resid 440 through 444 Processing helix chain '3' and resid 449 through 463 removed outlier: 3.588A pdb=" N VAL 3 453 " --> pdb=" O GLN 3 449 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 3 458 " --> pdb=" O THR 3 454 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS 3 459 " --> pdb=" O ALA 3 455 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 3 460 " --> pdb=" O ALA 3 456 " (cutoff:3.500A) Processing helix chain '3' and resid 481 through 485 Processing helix chain '3' and resid 489 through 500 removed outlier: 3.629A pdb=" N ALA 3 495 " --> pdb=" O LEU 3 491 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS 3 496 " --> pdb=" O TYR 3 492 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER 3 497 " --> pdb=" O ASN 3 493 " (cutoff:3.500A) Processing helix chain '3' and resid 615 through 619 Processing helix chain '3' and resid 621 through 634 removed outlier: 3.983A pdb=" N MET 3 627 " --> pdb=" O TYR 3 623 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 656 removed outlier: 4.058A pdb=" N LEU 3 643 " --> pdb=" O GLY 3 639 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR 3 650 " --> pdb=" O LYS 3 646 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS 3 653 " --> pdb=" O HIS 3 649 " (cutoff:3.500A) Processing helix chain '1' and resid 123 through 129 Processing helix chain '1' and resid 130 through 135 Processing helix chain '1' and resid 159 through 166 removed outlier: 3.567A pdb=" N LEU 1 162 " --> pdb=" O ASP 1 159 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP 1 165 " --> pdb=" O LEU 1 162 " (cutoff:3.500A) Processing helix chain '1' and resid 171 through 175 Processing helix chain '1' and resid 186 through 191 Processing helix chain '1' and resid 191 through 202 removed outlier: 4.051A pdb=" N ASP 1 197 " --> pdb=" O ASP 1 193 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 1 200 " --> pdb=" O GLU 1 196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN 1 202 " --> pdb=" O ILE 1 198 " (cutoff:3.500A) Processing helix chain '1' and resid 218 through 229 Processing helix chain '1' and resid 234 through 249 removed outlier: 3.658A pdb=" N LEU 1 238 " --> pdb=" O PHE 1 234 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG 1 239 " --> pdb=" O TRP 1 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 1 240 " --> pdb=" O HIS 1 236 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 1 242 " --> pdb=" O LEU 1 238 " (cutoff:3.500A) Processing helix chain '1' and resid 249 through 258 removed outlier: 3.584A pdb=" N LEU 1 256 " --> pdb=" O ARG 1 252 " (cutoff:3.500A) Processing helix chain '1' and resid 262 through 273 removed outlier: 3.573A pdb=" N TRP 1 266 " --> pdb=" O ASP 1 262 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU 1 267 " --> pdb=" O ALA 1 263 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 1 268 " --> pdb=" O ALA 1 264 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS 1 273 " --> pdb=" O ILE 1 269 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 299 Processing helix chain '1' and resid 308 through 314 Processing helix chain '1' and resid 328 through 333 removed outlier: 3.985A pdb=" N THR 1 333 " --> pdb=" O GLU 1 330 " (cutoff:3.500A) Processing helix chain '1' and resid 383 through 389 removed outlier: 3.725A pdb=" N LYS 1 387 " --> pdb=" O ASP 1 383 " (cutoff:3.500A) Processing helix chain '1' and resid 406 through 426 removed outlier: 3.831A pdb=" N LEU 1 410 " --> pdb=" O GLN 1 406 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG 1 412 " --> pdb=" O LYS 1 408 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL 1 420 " --> pdb=" O ALA 1 416 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP 1 423 " --> pdb=" O GLU 1 419 " (cutoff:3.500A) Processing helix chain '1' and resid 428 through 439 Processing helix chain '1' and resid 440 through 444 Processing helix chain '1' and resid 449 through 463 removed outlier: 3.588A pdb=" N VAL 1 453 " --> pdb=" O GLN 1 449 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 1 458 " --> pdb=" O THR 1 454 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS 1 459 " --> pdb=" O ALA 1 455 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 1 460 " --> pdb=" O ALA 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 481 through 485 Processing helix chain '1' and resid 489 through 500 removed outlier: 3.628A pdb=" N ALA 1 495 " --> pdb=" O LEU 1 491 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS 1 496 " --> pdb=" O TYR 1 492 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER 1 497 " --> pdb=" O ASN 1 493 " (cutoff:3.500A) Processing helix chain '1' and resid 615 through 619 Processing helix chain '1' and resid 621 through 634 removed outlier: 3.982A pdb=" N MET 1 627 " --> pdb=" O TYR 1 623 " (cutoff:3.500A) Processing helix chain '1' and resid 639 through 656 removed outlier: 4.059A pdb=" N LEU 1 643 " --> pdb=" O GLY 1 639 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR 1 650 " --> pdb=" O LYS 1 646 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS 1 653 " --> pdb=" O HIS 1 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.892A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS A 60 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 84 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 244 removed outlier: 6.551A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 542 removed outlier: 6.882A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 removed outlier: 5.586A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 removed outlier: 4.131A pdb=" N THR B 56 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.359A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.647A pdb=" N ILE B 146 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.624A pdb=" N LEU B 243 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 541 through 542 removed outlier: 6.623A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 69 through 70 removed outlier: 3.806A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS E 60 " --> pdb=" O SER E 101 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 26 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET E 84 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AB5, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AB6, first strand: chain 'E' and resid 241 through 244 removed outlier: 6.545A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 541 through 542 removed outlier: 3.502A pdb=" N ALA E 622 " --> pdb=" O PHE E 576 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 30 removed outlier: 5.567A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 56 through 57 removed outlier: 4.221A pdb=" N THR F 56 " --> pdb=" O CYS F 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.464A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 146 through 147 removed outlier: 3.508A pdb=" N ILE F 146 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS F 174 " --> pdb=" O ILE F 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 240 through 244 removed outlier: 6.012A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 541 through 542 removed outlier: 6.620A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.531A pdb=" N MET C 84 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C 26 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.811A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AC8, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'C' and resid 241 through 244 removed outlier: 6.412A pdb=" N ILE C 241 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR C 347 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU C 243 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.567A pdb=" N ALA C 622 " --> pdb=" O PHE C 576 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 27 through 30 removed outlier: 5.585A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 56 through 57 removed outlier: 4.147A pdb=" N THR D 56 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 115 through 118 removed outlier: 6.450A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 146 through 147 removed outlier: 3.637A pdb=" N ILE D 146 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.049A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 541 through 542 removed outlier: 6.722A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2' and resid 137 through 139 Processing sheet with id=AD9, first strand: chain '2' and resid 169 through 170 Processing sheet with id=AE1, first strand: chain '2' and resid 169 through 170 removed outlier: 3.630A pdb=" N CYS 2 344 " --> pdb=" O LEU 2 358 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE 2 304 " --> pdb=" O ILE 2 345 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TRP 2 347 " --> pdb=" O ILE 2 304 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU 2 306 " --> pdb=" O TRP 2 347 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '2' and resid 368 through 369 Processing sheet with id=AE3, first strand: chain '2' and resid 475 through 477 Processing sheet with id=AE4, first strand: chain '2' and resid 508 through 509 removed outlier: 3.965A pdb=" N VAL 2 525 " --> pdb=" O ASP 2 520 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '2' and resid 562 through 566 removed outlier: 7.043A pdb=" N THR 2 563 " --> pdb=" O PHE 2 579 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE 2 579 " --> pdb=" O THR 2 563 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER 2 565 " --> pdb=" O LYS 2 577 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '2' and resid 590 through 598 removed outlier: 3.741A pdb=" N GLU 2 590 " --> pdb=" O TRP 2 609 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU 2 605 " --> pdb=" O ILE 2 594 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '3' and resid 137 through 139 Processing sheet with id=AE8, first strand: chain '3' and resid 169 through 170 Processing sheet with id=AE9, first strand: chain '3' and resid 169 through 170 removed outlier: 3.629A pdb=" N CYS 3 344 " --> pdb=" O LEU 3 358 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE 3 304 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TRP 3 347 " --> pdb=" O ILE 3 304 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU 3 306 " --> pdb=" O TRP 3 347 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '3' and resid 368 through 369 Processing sheet with id=AF2, first strand: chain '3' and resid 475 through 477 Processing sheet with id=AF3, first strand: chain '3' and resid 508 through 509 removed outlier: 3.965A pdb=" N VAL 3 525 " --> pdb=" O ASP 3 520 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '3' and resid 562 through 566 removed outlier: 7.043A pdb=" N THR 3 563 " --> pdb=" O PHE 3 579 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N PHE 3 579 " --> pdb=" O THR 3 563 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER 3 565 " --> pdb=" O LYS 3 577 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '3' and resid 590 through 598 removed outlier: 3.740A pdb=" N GLU 3 590 " --> pdb=" O TRP 3 609 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU 3 605 " --> pdb=" O ILE 3 594 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '1' and resid 137 through 139 Processing sheet with id=AF7, first strand: chain '1' and resid 169 through 170 Processing sheet with id=AF8, first strand: chain '1' and resid 169 through 170 removed outlier: 3.630A pdb=" N CYS 1 344 " --> pdb=" O LEU 1 358 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE 1 304 " --> pdb=" O ILE 1 345 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TRP 1 347 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU 1 306 " --> pdb=" O TRP 1 347 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1' and resid 368 through 369 Processing sheet with id=AG1, first strand: chain '1' and resid 475 through 477 Processing sheet with id=AG2, first strand: chain '1' and resid 508 through 509 removed outlier: 3.965A pdb=" N VAL 1 525 " --> pdb=" O ASP 1 520 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '1' and resid 562 through 566 removed outlier: 7.042A pdb=" N THR 1 563 " --> pdb=" O PHE 1 579 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE 1 579 " --> pdb=" O THR 1 563 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER 1 565 " --> pdb=" O LYS 1 577 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '1' and resid 590 through 598 removed outlier: 3.741A pdb=" N GLU 1 590 " --> pdb=" O TRP 1 609 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU 1 605 " --> pdb=" O ILE 1 594 " (cutoff:3.500A) 1446 hydrogen bonds defined for protein. 4017 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: 15.47 Time building geometry restraints manager: 10.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 3 1.20 - 1.36: 17028 1.36 - 1.51: 15120 1.51 - 1.67: 17763 1.67 - 1.83: 405 Bond restraints: 50319 Sorted by residual: bond pdb=" CG PRO 2 328 " pdb=" CD PRO 2 328 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CG PRO 3 328 " pdb=" CD PRO 3 328 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CG PRO 1 328 " pdb=" CD PRO 1 328 " ideal model delta sigma weight residual 1.503 1.043 0.460 3.40e-02 8.65e+02 1.83e+02 bond pdb=" CA ALA F 15 " pdb=" C ALA F 15 " ideal model delta sigma weight residual 1.522 1.604 -0.082 1.31e-02 5.83e+03 3.94e+01 bond pdb=" CA ALA D 15 " pdb=" C ALA D 15 " ideal model delta sigma weight residual 1.520 1.604 -0.084 1.39e-02 5.18e+03 3.61e+01 ... (remaining 50314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.12: 67914 5.12 - 10.25: 83 10.25 - 15.37: 7 15.37 - 20.50: 9 20.50 - 25.62: 3 Bond angle restraints: 68016 Sorted by residual: angle pdb=" N PRO 1 328 " pdb=" CD PRO 1 328 " pdb=" CG PRO 1 328 " ideal model delta sigma weight residual 103.20 77.58 25.62 1.50e+00 4.44e-01 2.92e+02 angle pdb=" N PRO 2 328 " pdb=" CD PRO 2 328 " pdb=" CG PRO 2 328 " ideal model delta sigma weight residual 103.20 77.62 25.58 1.50e+00 4.44e-01 2.91e+02 angle pdb=" N PRO 3 328 " pdb=" CD PRO 3 328 " pdb=" CG PRO 3 328 " ideal model delta sigma weight residual 103.20 77.64 25.56 1.50e+00 4.44e-01 2.90e+02 angle pdb=" CA PRO 1 328 " pdb=" CB PRO 1 328 " pdb=" CG PRO 1 328 " ideal model delta sigma weight residual 104.50 84.76 19.74 1.90e+00 2.77e-01 1.08e+02 angle pdb=" CA PRO 2 328 " pdb=" CB PRO 2 328 " pdb=" CG PRO 2 328 " ideal model delta sigma weight residual 104.50 84.78 19.72 1.90e+00 2.77e-01 1.08e+02 ... (remaining 68011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 28384 17.80 - 35.61: 2151 35.61 - 53.41: 303 53.41 - 71.21: 57 71.21 - 89.02: 71 Dihedral angle restraints: 30966 sinusoidal: 12855 harmonic: 18111 Sorted by residual: dihedral pdb=" CA ALA C 596 " pdb=" C ALA C 596 " pdb=" N ALA C 597 " pdb=" CA ALA C 597 " ideal model delta harmonic sigma weight residual 180.00 130.17 49.83 0 5.00e+00 4.00e-02 9.93e+01 dihedral pdb=" CA ALA E 596 " pdb=" C ALA E 596 " pdb=" N ALA E 597 " pdb=" CA ALA E 597 " ideal model delta harmonic sigma weight residual 180.00 132.15 47.85 0 5.00e+00 4.00e-02 9.16e+01 dihedral pdb=" CA ALA A 596 " pdb=" C ALA A 596 " pdb=" N ALA A 597 " pdb=" CA ALA A 597 " ideal model delta harmonic sigma weight residual 180.00 132.96 47.04 0 5.00e+00 4.00e-02 8.85e+01 ... (remaining 30963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6422 0.067 - 0.134: 1082 0.134 - 0.201: 58 0.201 - 0.269: 0 0.269 - 0.336: 1 Chirality restraints: 7563 Sorted by residual: chirality pdb=" CB ILE F 342 " pdb=" CA ILE F 342 " pdb=" CG1 ILE F 342 " pdb=" CG2 ILE F 342 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA VAL D 514 " pdb=" N VAL D 514 " pdb=" C VAL D 514 " pdb=" CB VAL D 514 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB ILE C 342 " pdb=" CA ILE C 342 " pdb=" CG1 ILE C 342 " pdb=" CG2 ILE C 342 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 7560 not shown) Planarity restraints: 8982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 1 327 " 0.057 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO 1 328 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO 1 328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 1 328 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 2 327 " -0.056 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO 2 328 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO 2 328 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO 2 328 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 327 " 0.056 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO 3 328 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO 3 328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 3 328 " 0.043 5.00e-02 4.00e+02 ... (remaining 8979 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 770 2.64 - 3.21: 47230 3.21 - 3.77: 71485 3.77 - 4.34: 103350 4.34 - 4.90: 162146 Nonbonded interactions: 384981 Sorted by model distance: nonbonded pdb=" OH TYR B 244 " pdb=" OE1 GLN B 568 " model vdw 2.076 3.040 nonbonded pdb=" O GLN 2 501 " pdb=" OH TYR 2 508 " model vdw 2.090 3.040 nonbonded pdb=" O GLN 1 501 " pdb=" OH TYR 1 508 " model vdw 2.090 3.040 nonbonded pdb=" O GLN 3 501 " pdb=" OH TYR 3 508 " model vdw 2.090 3.040 nonbonded pdb=" OH TYR D 244 " pdb=" OE1 GLN D 568 " model vdw 2.115 3.040 ... (remaining 384976 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: 0.04 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' } ncs_group { reference = (chain 'A' and (resid 12 through 744 or resid 746 through 775)) selection = (chain 'B' and (resid 12 through 744 or resid 746 through 775)) selection = (chain 'C' and (resid 12 through 744 or resid 746 through 775)) selection = (chain 'D' and (resid 12 through 744 or resid 746 through 775)) selection = (chain 'E' and (resid 12 through 744 or resid 746 through 775)) selection = (chain 'F' and (resid 12 through 744 or resid 746 through 775)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.400 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 95.960 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.230 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:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.006 0.460 50319 Z= 0.423 Angle : 0.813 25.624 68016 Z= 0.464 Chirality : 0.048 0.336 7563 Planarity : 0.005 0.078 8982 Dihedral : 13.490 89.017 19278 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 0.24 % Allowed : 0.37 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.11), residues: 6279 helix: -2.13 (0.10), residues: 2250 sheet: -2.10 (0.19), residues: 708 loop : -1.16 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 3 580 HIS 0.004 0.001 HIS 3 300 PHE 0.021 0.002 PHE C 771 TYR 0.036 0.002 TYR 1 608 ARG 0.012 0.001 ARG D 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 347 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 GLN cc_start: 0.4834 (OUTLIER) cc_final: 0.3694 (mm-40) REVERT: B 158 MET cc_start: 0.5788 (mmm) cc_final: 0.4913 (pmm) REVERT: E 751 ASP cc_start: 0.7738 (t70) cc_final: 0.7467 (t0) REVERT: D 740 MET cc_start: 0.8149 (mmm) cc_final: 0.7881 (mmm) REVERT: 2 303 ILE cc_start: 0.0772 (mt) cc_final: 0.0557 (mm) REVERT: 1 303 ILE cc_start: 0.0752 (mt) cc_final: 0.0483 (mm) outliers start: 13 outliers final: 9 residues processed: 349 average time/residue: 0.4812 time to fit residues: 284.8632 Evaluate side-chains 286 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain 2 residue 422 MET Chi-restraints excluded: chain 2 residue 642 ILE Chi-restraints excluded: chain 2 residue 657 LYS Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 642 ILE Chi-restraints excluded: chain 3 residue 657 LYS Chi-restraints excluded: chain 1 residue 422 MET Chi-restraints excluded: chain 1 residue 642 ILE Chi-restraints excluded: chain 1 residue 657 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 30.0000 chunk 472 optimal weight: 50.0000 chunk 262 optimal weight: 0.7980 chunk 161 optimal weight: 9.9990 chunk 319 optimal weight: 0.3980 chunk 252 optimal weight: 0.6980 chunk 489 optimal weight: 40.0000 chunk 189 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 364 optimal weight: 0.9990 chunk 566 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 GLN B 19 GLN B 21 ASN B 36 ASN F 36 ASN F 538 ASN D 36 ASN D 260 ASN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 764 GLN 2 126 HIS 2 174 HIS ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 245 HIS ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 174 HIS 1 245 HIS ** 1 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.185167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.138954 restraints weight = 153411.485| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 6.41 r_work: 0.3323 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 50319 Z= 0.202 Angle : 0.674 9.796 68016 Z= 0.349 Chirality : 0.048 0.263 7563 Planarity : 0.005 0.065 8982 Dihedral : 5.825 58.886 6885 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.89 % Favored : 93.08 % Rotamer: Outliers : 0.24 % Allowed : 3.71 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 6279 helix: -1.55 (0.10), residues: 2238 sheet: -1.90 (0.19), residues: 702 loop : -1.06 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 1 266 HIS 0.007 0.001 HIS 2 174 PHE 0.015 0.001 PHE A 771 TYR 0.037 0.002 TYR F 244 ARG 0.007 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 346 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.5893 (mmm) cc_final: 0.5034 (pmm) REVERT: E 351 ASN cc_start: 0.8634 (m-40) cc_final: 0.8356 (m110) REVERT: E 442 MET cc_start: 0.7930 (mpp) cc_final: 0.6182 (tpt) REVERT: F 678 MET cc_start: 0.8331 (mmt) cc_final: 0.7994 (mpp) REVERT: C 364 ASP cc_start: 0.8298 (p0) cc_final: 0.8054 (p0) REVERT: C 700 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7815 (mtp-110) REVERT: D 649 ASP cc_start: 0.8308 (p0) cc_final: 0.8073 (p0) REVERT: 2 174 HIS cc_start: 0.1637 (m90) cc_final: 0.0991 (m-70) REVERT: 2 250 LEU cc_start: 0.1570 (OUTLIER) cc_final: 0.1255 (pp) REVERT: 3 254 GLN cc_start: -0.2180 (mt0) cc_final: -0.2688 (mm-40) REVERT: 3 323 LEU cc_start: 0.4734 (mt) cc_final: 0.4520 (mp) REVERT: 1 174 HIS cc_start: 0.1729 (m90) cc_final: 0.1294 (m-70) REVERT: 1 254 GLN cc_start: -0.1819 (mt0) cc_final: -0.2252 (mm-40) outliers start: 13 outliers final: 2 residues processed: 351 average time/residue: 0.4989 time to fit residues: 294.1272 Evaluate side-chains 284 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 281 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain 2 residue 250 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 174 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 580 optimal weight: 50.0000 chunk 366 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 459 optimal weight: 0.0040 chunk 616 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 chunk 603 optimal weight: 20.0000 chunk 619 optimal weight: 3.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS ** E 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.182460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135818 restraints weight = 147484.994| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 5.23 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 50319 Z= 0.391 Angle : 0.690 8.113 68016 Z= 0.351 Chirality : 0.049 0.266 7563 Planarity : 0.005 0.060 8982 Dihedral : 5.539 45.927 6855 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.95 % Rotamer: Outliers : 0.75 % Allowed : 5.29 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 6279 helix: -1.42 (0.11), residues: 2310 sheet: -1.87 (0.19), residues: 720 loop : -1.09 (0.11), residues: 3249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 266 HIS 0.008 0.001 HIS 1 300 PHE 0.020 0.002 PHE F 360 TYR 0.041 0.002 TYR B 244 ARG 0.007 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 4.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8287 (mmm) cc_final: 0.7896 (mmm) REVERT: B 158 MET cc_start: 0.5586 (mmm) cc_final: 0.5009 (pmm) REVERT: E 442 MET cc_start: 0.7803 (mpp) cc_final: 0.5748 (tpt) REVERT: 2 250 LEU cc_start: 0.2368 (OUTLIER) cc_final: 0.1844 (pp) REVERT: 2 417 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.3431 (mmt) REVERT: 3 254 GLN cc_start: -0.0841 (mt0) cc_final: -0.2196 (mm110) REVERT: 3 417 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.4714 (mmt) REVERT: 1 180 TYR cc_start: 0.4569 (OUTLIER) cc_final: 0.2981 (t80) REVERT: 1 254 GLN cc_start: -0.0948 (mt0) cc_final: -0.2046 (mm-40) outliers start: 40 outliers final: 24 residues processed: 303 average time/residue: 0.4641 time to fit residues: 241.6162 Evaluate side-chains 295 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 2 residue 642 ILE Chi-restraints excluded: chain 3 residue 209 ILE Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 642 ILE Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 209 ILE Chi-restraints excluded: chain 1 residue 261 ILE Chi-restraints excluded: chain 1 residue 303 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 525 optimal weight: 20.0000 chunk 370 optimal weight: 0.9990 chunk 494 optimal weight: 20.0000 chunk 342 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 chunk 600 optimal weight: 30.0000 chunk 206 optimal weight: 0.0970 chunk 110 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.186196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139621 restraints weight = 146658.514| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 6.26 r_work: 0.3325 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 50319 Z= 0.192 Angle : 0.594 12.025 68016 Z= 0.304 Chirality : 0.046 0.258 7563 Planarity : 0.004 0.058 8982 Dihedral : 5.186 39.660 6855 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.50 % Allowed : 6.66 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 6279 helix: -1.16 (0.11), residues: 2304 sheet: -1.73 (0.19), residues: 714 loop : -0.92 (0.12), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 551 HIS 0.008 0.001 HIS 2 300 PHE 0.023 0.001 PHE F 674 TYR 0.035 0.001 TYR B 244 ARG 0.006 0.000 ARG E 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 4.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.8017 (tpp) cc_final: 0.7312 (tpp) REVERT: A 740 MET cc_start: 0.8830 (mmm) cc_final: 0.8417 (mmm) REVERT: B 158 MET cc_start: 0.5806 (mmm) cc_final: 0.5036 (pmm) REVERT: E 442 MET cc_start: 0.7839 (mpp) cc_final: 0.5937 (tpt) REVERT: E 740 MET cc_start: 0.8763 (mmm) cc_final: 0.8385 (mmm) REVERT: C 315 LYS cc_start: 0.7520 (mtmt) cc_final: 0.6770 (tmtt) REVERT: C 442 MET cc_start: 0.8042 (mmm) cc_final: 0.7421 (mmt) REVERT: D 366 GLU cc_start: 0.8348 (pp20) cc_final: 0.7808 (pp20) REVERT: 2 250 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.1006 (pp) REVERT: 3 254 GLN cc_start: -0.1939 (mt0) cc_final: -0.2571 (mm110) REVERT: 3 417 MET cc_start: 0.4782 (OUTLIER) cc_final: 0.4324 (mmt) REVERT: 1 180 TYR cc_start: 0.3582 (OUTLIER) cc_final: 0.2864 (t80) REVERT: 1 254 GLN cc_start: -0.2073 (mt0) cc_final: -0.2594 (mm-40) outliers start: 27 outliers final: 16 residues processed: 312 average time/residue: 0.5042 time to fit residues: 268.4251 Evaluate side-chains 300 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 281 time to evaluate : 4.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 261 ILE Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 147 optimal weight: 7.9990 chunk 287 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 456 optimal weight: 9.9990 chunk 519 optimal weight: 50.0000 chunk 443 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 512 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 499 optimal weight: 20.0000 chunk 202 optimal weight: 0.0040 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS F 398 GLN F 641 GLN D 340 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4527 r_free = 0.4527 target = 0.182899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.136112 restraints weight = 146500.447| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 6.44 r_work: 0.3264 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 50319 Z= 0.361 Angle : 0.647 10.197 68016 Z= 0.327 Chirality : 0.048 0.245 7563 Planarity : 0.005 0.058 8982 Dihedral : 5.236 43.667 6855 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.03 % Allowed : 7.20 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 6279 helix: -1.10 (0.11), residues: 2289 sheet: -1.80 (0.19), residues: 723 loop : -0.94 (0.12), residues: 3267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 347 HIS 0.009 0.001 HIS 1 300 PHE 0.020 0.002 PHE F 360 TYR 0.034 0.002 TYR B 244 ARG 0.006 0.000 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6465 (t70) REVERT: B 158 MET cc_start: 0.5804 (mmm) cc_final: 0.5029 (pmm) REVERT: E 340 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.6537 (t70) REVERT: E 442 MET cc_start: 0.7921 (mpp) cc_final: 0.5704 (tpt) REVERT: E 449 MET cc_start: 0.8206 (tpp) cc_final: 0.7821 (tpp) REVERT: E 649 ASP cc_start: 0.7981 (p0) cc_final: 0.7747 (p0) REVERT: E 652 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7753 (t) REVERT: E 740 MET cc_start: 0.8687 (mmm) cc_final: 0.8265 (mmm) REVERT: F 332 MET cc_start: 0.8872 (tpp) cc_final: 0.8630 (tpp) REVERT: F 340 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6897 (t-90) REVERT: C 340 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6566 (t70) REVERT: C 442 MET cc_start: 0.7917 (mmm) cc_final: 0.7212 (mmt) REVERT: C 649 ASP cc_start: 0.8148 (p0) cc_final: 0.7920 (p0) REVERT: D 366 GLU cc_start: 0.8652 (pp20) cc_final: 0.8421 (pp20) REVERT: 3 254 GLN cc_start: -0.2260 (mt0) cc_final: -0.2746 (mm110) REVERT: 3 417 MET cc_start: 0.4767 (OUTLIER) cc_final: 0.4447 (mmt) REVERT: 1 180 TYR cc_start: 0.3588 (OUTLIER) cc_final: 0.3090 (t80) REVERT: 1 254 GLN cc_start: -0.2128 (mt0) cc_final: -0.2629 (mm-40) outliers start: 55 outliers final: 36 residues processed: 310 average time/residue: 0.4692 time to fit residues: 251.1742 Evaluate side-chains 312 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 261 ILE Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 2 residue 642 ILE Chi-restraints excluded: chain 3 residue 209 ILE Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 642 ILE Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 209 ILE Chi-restraints excluded: chain 1 residue 261 ILE Chi-restraints excluded: chain 1 residue 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 344 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 318 optimal weight: 20.0000 chunk 372 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 386 optimal weight: 7.9990 chunk 327 optimal weight: 0.3980 chunk 567 optimal weight: 8.9990 chunk 296 optimal weight: 0.6980 chunk 549 optimal weight: 30.0000 chunk 470 optimal weight: 40.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 421 GLN D 226 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4589 r_free = 0.4589 target = 0.187268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.140635 restraints weight = 141661.409| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 5.69 r_work: 0.3366 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 50319 Z= 0.163 Angle : 0.571 9.118 68016 Z= 0.291 Chirality : 0.045 0.293 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.934 38.745 6855 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.65 % Allowed : 8.04 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 6279 helix: -0.88 (0.11), residues: 2292 sheet: -1.65 (0.19), residues: 714 loop : -0.81 (0.12), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.009 0.001 HIS 3 300 PHE 0.017 0.001 PHE B 674 TYR 0.033 0.001 TYR B 244 ARG 0.004 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7921 (tpp) cc_final: 0.7270 (tpp) REVERT: B 158 MET cc_start: 0.5930 (mmm) cc_final: 0.5127 (pmm) REVERT: E 340 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6497 (t70) REVERT: E 442 MET cc_start: 0.7776 (mpp) cc_final: 0.5654 (tpt) REVERT: E 449 MET cc_start: 0.8171 (tpp) cc_final: 0.7814 (tpp) REVERT: E 649 ASP cc_start: 0.7940 (p0) cc_final: 0.7663 (p0) REVERT: E 652 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7433 (t) REVERT: E 740 MET cc_start: 0.8636 (mmm) cc_final: 0.8192 (mmm) REVERT: C 364 ASP cc_start: 0.8215 (p0) cc_final: 0.7985 (p0) REVERT: C 442 MET cc_start: 0.7728 (mmm) cc_final: 0.6965 (mmt) REVERT: C 649 ASP cc_start: 0.7982 (p0) cc_final: 0.7763 (p0) REVERT: 2 250 LEU cc_start: 0.1636 (OUTLIER) cc_final: 0.1286 (pp) REVERT: 3 254 GLN cc_start: -0.2171 (mt0) cc_final: -0.2751 (mm-40) REVERT: 3 417 MET cc_start: 0.5023 (OUTLIER) cc_final: 0.4514 (mmt) REVERT: 1 180 TYR cc_start: 0.3529 (OUTLIER) cc_final: 0.2943 (t80) REVERT: 1 254 GLN cc_start: -0.2038 (mt0) cc_final: -0.2579 (mm-40) outliers start: 35 outliers final: 22 residues processed: 309 average time/residue: 0.4877 time to fit residues: 261.9201 Evaluate side-chains 296 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 261 ILE Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 156 optimal weight: 20.0000 chunk 573 optimal weight: 0.9980 chunk 525 optimal weight: 0.7980 chunk 341 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 563 optimal weight: 0.8980 chunk 434 optimal weight: 0.1980 chunk 330 optimal weight: 2.9990 chunk 531 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS B 398 GLN B 568 GLN F 340 HIS D 340 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4590 r_free = 0.4590 target = 0.187210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.141204 restraints weight = 153044.755| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 5.35 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50319 Z= 0.181 Angle : 0.561 8.564 68016 Z= 0.285 Chirality : 0.045 0.259 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.777 42.845 6855 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.69 % Allowed : 8.39 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 6279 helix: -0.71 (0.11), residues: 2292 sheet: -1.57 (0.20), residues: 696 loop : -0.77 (0.12), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 551 HIS 0.006 0.001 HIS 3 300 PHE 0.018 0.001 PHE B 674 TYR 0.033 0.001 TYR B 244 ARG 0.004 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7441 (tmm) cc_final: 0.7225 (tmm) REVERT: A 442 MET cc_start: 0.7773 (mpp) cc_final: 0.7508 (mpp) REVERT: B 158 MET cc_start: 0.5755 (mmm) cc_final: 0.5293 (pmm) REVERT: E 340 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.5918 (t70) REVERT: E 442 MET cc_start: 0.7586 (mpp) cc_final: 0.5246 (tpt) REVERT: E 449 MET cc_start: 0.7663 (tpp) cc_final: 0.7429 (tpp) REVERT: E 652 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7444 (t) REVERT: E 740 MET cc_start: 0.8031 (mmm) cc_final: 0.7569 (mmm) REVERT: F 340 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.6187 (t-90) REVERT: C 442 MET cc_start: 0.7499 (mmm) cc_final: 0.6865 (mmt) REVERT: 3 254 GLN cc_start: -0.0962 (mt0) cc_final: -0.2176 (mm-40) REVERT: 1 180 TYR cc_start: 0.4153 (OUTLIER) cc_final: 0.3326 (t80) REVERT: 1 254 GLN cc_start: -0.1095 (mt0) cc_final: -0.2086 (mm-40) outliers start: 37 outliers final: 23 residues processed: 314 average time/residue: 0.4682 time to fit residues: 254.0153 Evaluate side-chains 295 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 456 optimal weight: 0.0870 chunk 139 optimal weight: 0.7980 chunk 401 optimal weight: 3.9990 chunk 158 optimal weight: 50.0000 chunk 314 optimal weight: 7.9990 chunk 588 optimal weight: 5.9990 chunk 305 optimal weight: 3.9990 chunk 568 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 484 optimal weight: 20.0000 chunk 565 optimal weight: 4.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 568 GLN F 340 HIS ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4550 r_free = 0.4550 target = 0.185373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133501 restraints weight = 140720.623| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 6.10 r_work: 0.3311 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 50319 Z= 0.314 Angle : 0.617 8.928 68016 Z= 0.312 Chirality : 0.047 0.339 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.886 45.974 6855 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.86 % Allowed : 8.80 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 6279 helix: -0.76 (0.11), residues: 2289 sheet: -1.61 (0.20), residues: 699 loop : -0.80 (0.12), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 580 HIS 0.005 0.001 HIS 3 300 PHE 0.030 0.002 PHE B 674 TYR 0.026 0.001 TYR F 244 ARG 0.005 0.000 ARG 3 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 4.149 Fit side-chains revert: symmetry clash REVERT: A 449 MET cc_start: 0.7918 (tpp) cc_final: 0.7335 (tpp) REVERT: A 488 GLU cc_start: 0.8639 (tt0) cc_final: 0.8353 (tt0) REVERT: B 158 MET cc_start: 0.6120 (mmm) cc_final: 0.5248 (pmm) REVERT: B 568 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: E 340 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6443 (t70) REVERT: E 442 MET cc_start: 0.7867 (mpp) cc_final: 0.5666 (tpt) REVERT: E 652 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7627 (t) REVERT: F 340 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6659 (t-90) REVERT: C 442 MET cc_start: 0.7691 (mmm) cc_final: 0.6992 (mmt) REVERT: 3 254 GLN cc_start: -0.2204 (mt0) cc_final: -0.2687 (mm-40) REVERT: 3 417 MET cc_start: 0.4955 (OUTLIER) cc_final: 0.4586 (mmt) REVERT: 3 493 ASN cc_start: 0.6362 (p0) cc_final: 0.6044 (m-40) REVERT: 1 180 TYR cc_start: 0.3267 (OUTLIER) cc_final: 0.2959 (t80) REVERT: 1 254 GLN cc_start: -0.2248 (mt0) cc_final: -0.2749 (mm-40) REVERT: 1 422 MET cc_start: 0.4401 (mmm) cc_final: 0.4170 (mmm) outliers start: 46 outliers final: 35 residues processed: 302 average time/residue: 0.4703 time to fit residues: 247.1333 Evaluate side-chains 310 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 568 GLN Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 209 ILE Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 549 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 443 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 243 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 547 optimal weight: 4.9990 chunk 545 optimal weight: 20.0000 chunk 558 optimal weight: 9.9990 chunk 578 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 340 HIS F 340 HIS D 340 HIS ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4510 r_free = 0.4510 target = 0.182264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131667 restraints weight = 123753.673| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 4.70 r_work: 0.3324 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 50319 Z= 0.413 Angle : 0.672 8.294 68016 Z= 0.340 Chirality : 0.049 0.343 7563 Planarity : 0.005 0.056 8982 Dihedral : 5.088 49.432 6855 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.03 % Allowed : 8.82 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 6279 helix: -0.91 (0.11), residues: 2298 sheet: -1.77 (0.19), residues: 708 loop : -0.88 (0.12), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 580 HIS 0.009 0.001 HIS F 340 PHE 0.025 0.002 PHE B 674 TYR 0.026 0.002 TYR E 244 ARG 0.007 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 4.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6357 (t70) REVERT: A 488 GLU cc_start: 0.8473 (tt0) cc_final: 0.8157 (tt0) REVERT: B 158 MET cc_start: 0.6066 (mmm) cc_final: 0.5191 (pmm) REVERT: E 340 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6505 (t70) REVERT: E 442 MET cc_start: 0.7817 (mpp) cc_final: 0.5516 (tpt) REVERT: E 449 MET cc_start: 0.8110 (tpp) cc_final: 0.7763 (tpp) REVERT: E 652 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.7768 (t) REVERT: E 740 MET cc_start: 0.8589 (mmm) cc_final: 0.8013 (mmm) REVERT: F 340 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6782 (t-90) REVERT: C 340 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6412 (t70) REVERT: C 442 MET cc_start: 0.7775 (mmm) cc_final: 0.7016 (mmt) REVERT: D 366 GLU cc_start: 0.8648 (pp20) cc_final: 0.8355 (pp20) REVERT: 3 254 GLN cc_start: -0.1845 (mt0) cc_final: -0.2528 (mm-40) REVERT: 3 417 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.4535 (mmt) REVERT: 3 493 ASN cc_start: 0.6196 (p0) cc_final: 0.5879 (m-40) REVERT: 1 180 TYR cc_start: 0.3520 (OUTLIER) cc_final: 0.2917 (t80) REVERT: 1 254 GLN cc_start: -0.2066 (mt0) cc_final: -0.2697 (mm-40) outliers start: 55 outliers final: 41 residues processed: 302 average time/residue: 0.4497 time to fit residues: 237.3135 Evaluate side-chains 312 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 340 HIS Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 340 HIS Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 731 ILE Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 209 ILE Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 1 residue 139 MET Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 409 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 338 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 37 optimal weight: 0.9980 chunk 540 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 472 optimal weight: 40.0000 chunk 412 optimal weight: 0.9980 chunk 603 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS B 568 GLN E 641 GLN F 340 HIS ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 436 HIS ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 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 = 0.4592 r_free = 0.4592 target = 0.187827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.137783 restraints weight = 132115.687| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 5.19 r_work: 0.3391 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 50319 Z= 0.168 Angle : 0.581 8.897 68016 Z= 0.295 Chirality : 0.045 0.312 7563 Planarity : 0.004 0.058 8982 Dihedral : 4.810 46.042 6855 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.63 % Allowed : 9.23 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.11), residues: 6279 helix: -0.71 (0.11), residues: 2307 sheet: -1.57 (0.20), residues: 687 loop : -0.76 (0.12), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.047 0.001 HIS F 340 PHE 0.023 0.001 PHE B 674 TYR 0.028 0.001 TYR F 244 ARG 0.009 0.000 ARG C 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12558 Ramachandran restraints generated. 6279 Oldfield, 0 Emsley, 6279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6436 (t70) REVERT: A 449 MET cc_start: 0.7902 (tpp) cc_final: 0.7231 (tpp) REVERT: A 488 GLU cc_start: 0.8649 (tt0) cc_final: 0.8328 (tt0) REVERT: B 158 MET cc_start: 0.6036 (mmm) cc_final: 0.5213 (pmm) REVERT: E 340 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.6491 (t70) REVERT: E 442 MET cc_start: 0.7817 (mpp) cc_final: 0.5642 (tpt) REVERT: E 449 MET cc_start: 0.8087 (tpp) cc_final: 0.7783 (tpp) REVERT: E 740 MET cc_start: 0.8635 (mmm) cc_final: 0.8104 (mmm) REVERT: C 442 MET cc_start: 0.7765 (mmm) cc_final: 0.7132 (mmt) REVERT: C 720 MET cc_start: 0.6028 (ttp) cc_final: 0.5827 (ttp) REVERT: 3 254 GLN cc_start: -0.1873 (mt0) cc_final: -0.2486 (mm-40) REVERT: 3 417 MET cc_start: 0.5028 (OUTLIER) cc_final: 0.4518 (mmt) REVERT: 3 422 MET cc_start: 0.4725 (mmm) cc_final: 0.4263 (mmm) REVERT: 1 180 TYR cc_start: 0.3275 (OUTLIER) cc_final: 0.2833 (t80) REVERT: 1 254 GLN cc_start: -0.1772 (mt0) cc_final: -0.2473 (mm-40) REVERT: 1 312 MET cc_start: -0.0034 (mmt) cc_final: -0.1705 (mmt) outliers start: 34 outliers final: 23 residues processed: 293 average time/residue: 0.4617 time to fit residues: 234.2966 Evaluate side-chains 294 residues out of total 5352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 267 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 1 residue 180 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 29 optimal weight: 0.7980 chunk 491 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 585 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 341 optimal weight: 0.8980 chunk 483 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 377 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS E 641 GLN F 340 HIS D 340 HIS ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.186657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.136596 restraints weight = 138775.272| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 5.66 r_work: 0.3359 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 50319 Z= 0.237 Angle : 0.588 10.282 68016 Z= 0.297 Chirality : 0.046 0.325 7563 Planarity : 0.004 0.057 8982 Dihedral : 4.771 46.417 6855 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.65 % Allowed : 9.38 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.11), residues: 6279 helix: -0.63 (0.11), residues: 2292 sheet: -1.49 (0.20), residues: 675 loop : -0.76 (0.12), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 551 HIS 0.005 0.001 HIS 3 300 PHE 0.026 0.001 PHE B 674 TYR 0.022 0.001 TYR B 244 ARG 0.005 0.000 ARG C 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23691.57 seconds wall clock time: 406 minutes 36.69 seconds (24396.69 seconds total)