Starting phenix.real_space_refine on Thu Oct 10 04:00:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_39360.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_39360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_39360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_39360.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yka_39360/10_2024/8yka_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 32.39, per 1000 atoms: 0.66 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: 9.06 Conformation dependent library (CDL) restraints added in 8.0 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: 4.45 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: 15.63 Time building geometry restraints manager: 10.75 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: 0.00 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: 1.680 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: 0.050 Extract box with map and model: 1.520 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 97.350 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.240 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: 105.060 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 13 poor density : 347 time to evaluate : 4.307 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: 0.4680 time to fit residues: 281.4262 Evaluate side-chains 286 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 276 time to evaluate : 4.365 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 fitting. rotamer outliers: 13 poor density : 346 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.5782 (mmm) cc_final: 0.5147 (pmm) REVERT: E 442 MET cc_start: 0.7638 (mpp) cc_final: 0.5840 (tpt) REVERT: D 740 MET cc_start: 0.8017 (mmm) cc_final: 0.7817 (mmm) REVERT: 2 174 HIS cc_start: 0.1038 (m90) cc_final: 0.0753 (m-70) REVERT: 2 250 LEU cc_start: 0.2485 (OUTLIER) cc_final: 0.1843 (pp) REVERT: 3 254 GLN cc_start: -0.1108 (mt0) cc_final: -0.2248 (mm-40) REVERT: 1 254 GLN cc_start: -0.1036 (mt0) cc_final: -0.1942 (mm-40) outliers start: 13 outliers final: 2 residues processed: 351 average time/residue: 0.4626 time to fit residues: 276.1931 Evaluate side-chains 282 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 279 time to evaluate : 4.266 ------------------------------------------------------------------------------- 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 314 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 471 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 567 optimal weight: 0.9990 chunk 613 optimal weight: 6.9990 chunk 505 optimal weight: 0.8980 chunk 562 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 455 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS E 351 ASN F 568 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 50319 Z= 0.256 Angle : 0.624 7.976 68016 Z= 0.320 Chirality : 0.047 0.264 7563 Planarity : 0.005 0.059 8982 Dihedral : 5.324 42.738 6855 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer: Outliers : 0.67 % Allowed : 5.26 % Favored : 94.07 % 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: -1.91 (0.11), residues: 6279 helix: -1.32 (0.11), residues: 2301 sheet: -1.75 (0.19), residues: 714 loop : -0.99 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 551 HIS 0.007 0.001 HIS 1 300 PHE 0.019 0.001 PHE F 674 TYR 0.037 0.002 TYR B 244 ARG 0.006 0.000 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 331 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 4.295 Fit side-chains revert: symmetry clash REVERT: A 611 MET cc_start: 0.8412 (ttm) cc_final: 0.8210 (ttp) REVERT: A 740 MET cc_start: 0.8179 (mmm) cc_final: 0.7776 (mmm) REVERT: B 158 MET cc_start: 0.5565 (mmm) cc_final: 0.4990 (pmm) REVERT: E 442 MET cc_start: 0.7784 (mpp) cc_final: 0.5949 (tpt) REVERT: 2 250 LEU cc_start: 0.2321 (OUTLIER) cc_final: 0.1844 (pp) REVERT: 2 417 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.3415 (mmt) REVERT: 3 254 GLN cc_start: -0.0723 (mt0) cc_final: -0.2119 (mm110) REVERT: 3 417 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.4735 (mmt) REVERT: 1 180 TYR cc_start: 0.4203 (OUTLIER) cc_final: 0.2721 (t80) REVERT: 1 254 GLN cc_start: -0.0821 (mt0) cc_final: -0.1922 (mm-40) outliers start: 36 outliers final: 19 residues processed: 312 average time/residue: 0.4560 time to fit residues: 245.4349 Evaluate side-chains 298 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 4.257 ------------------------------------------------------------------------------- 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 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 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 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 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 560 optimal weight: 4.9990 chunk 426 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 381 optimal weight: 20.0000 chunk 569 optimal weight: 40.0000 chunk 603 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 539 optimal weight: 40.0000 chunk 162 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 398 GLN ** 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** ** 2 289 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 50319 Z= 0.364 Angle : 0.663 11.360 68016 Z= 0.336 Chirality : 0.049 0.282 7563 Planarity : 0.005 0.059 8982 Dihedral : 5.347 42.748 6855 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.76 % Allowed : 6.47 % Favored : 92.77 % 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: -1.83 (0.11), residues: 6279 helix: -1.20 (0.11), residues: 2262 sheet: -1.81 (0.19), residues: 723 loop : -0.97 (0.11), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 347 HIS 0.009 0.001 HIS 2 300 PHE 0.020 0.002 PHE F 360 TYR 0.037 0.002 TYR B 244 ARG 0.006 0.000 ARG F 349 *********************** 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 323 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 282 time to evaluate : 4.307 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.5586 (mmm) cc_final: 0.5012 (pmm) REVERT: E 340 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5658 (t70) REVERT: E 442 MET cc_start: 0.7603 (mpp) cc_final: 0.5473 (tpt) REVERT: E 740 MET cc_start: 0.8028 (mmm) cc_final: 0.7693 (mmm) REVERT: C 442 MET cc_start: 0.7661 (mmm) cc_final: 0.6979 (mmt) REVERT: 2 417 MET cc_start: 0.4829 (OUTLIER) cc_final: 0.3313 (mmt) REVERT: 3 254 GLN cc_start: -0.0724 (mt0) cc_final: -0.2116 (mm110) REVERT: 3 417 MET cc_start: 0.5281 (OUTLIER) cc_final: 0.4432 (mmt) REVERT: 1 180 TYR cc_start: 0.4094 (OUTLIER) cc_final: 0.3140 (t80) REVERT: 1 254 GLN cc_start: -0.1098 (mt0) cc_final: -0.2121 (mm-40) REVERT: 1 422 MET cc_start: 0.3319 (mmm) cc_final: 0.3109 (mmm) outliers start: 41 outliers final: 30 residues processed: 304 average time/residue: 0.4590 time to fit residues: 242.2838 Evaluate side-chains 301 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 267 time to evaluate : 4.301 ------------------------------------------------------------------------------- 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 330 THR Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain E residue 244 TYR 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 F residue 309 ILE 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 275 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 590 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 8 optimal weight: 40.0000 chunk 449 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 514 optimal weight: 50.0000 chunk 416 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 307 optimal weight: 5.9990 chunk 541 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** F 568 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 3 300 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 50319 Z= 0.342 Angle : 0.639 10.268 68016 Z= 0.325 Chirality : 0.048 0.286 7563 Planarity : 0.005 0.059 8982 Dihedral : 5.278 40.881 6855 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.97 % Allowed : 7.46 % Favored : 91.57 % 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: -1.79 (0.11), residues: 6279 helix: -1.14 (0.11), residues: 2271 sheet: -1.85 (0.19), residues: 723 loop : -0.95 (0.11), residues: 3285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.008 0.001 HIS 3 300 PHE 0.018 0.002 PHE D 360 TYR 0.034 0.002 TYR B 244 ARG 0.005 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 328 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 4.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5634 (t70) REVERT: A 442 MET cc_start: 0.7395 (mpp) cc_final: 0.7055 (mpp) REVERT: B 158 MET cc_start: 0.5572 (mmm) cc_final: 0.5054 (pmm) REVERT: E 340 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5652 (t70) REVERT: E 442 MET cc_start: 0.7646 (mpp) cc_final: 0.5380 (tpt) REVERT: E 652 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7342 (t) REVERT: E 740 MET cc_start: 0.8007 (mmm) cc_final: 0.7638 (mmm) REVERT: F 340 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.6020 (t-90) REVERT: C 340 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.5513 (t70) REVERT: C 442 MET cc_start: 0.7671 (mmm) cc_final: 0.7059 (mmt) REVERT: 3 254 GLN cc_start: -0.0875 (mt0) cc_final: -0.2242 (mm110) REVERT: 3 417 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.4814 (mmt) REVERT: 1 180 TYR cc_start: 0.4135 (OUTLIER) cc_final: 0.3320 (t80) REVERT: 1 254 GLN cc_start: -0.1081 (mt0) cc_final: -0.2134 (mm-40) outliers start: 52 outliers final: 37 residues processed: 302 average time/residue: 0.4558 time to fit residues: 242.3796 Evaluate side-chains 309 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 265 time to evaluate : 4.338 ------------------------------------------------------------------------------- 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 244 TYR 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 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 590 ILE 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 D residue 447 VAL 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 642 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.0870 chunk 543 optimal weight: 40.0000 chunk 119 optimal weight: 0.8980 chunk 354 optimal weight: 0.0570 chunk 148 optimal weight: 0.7980 chunk 603 optimal weight: 20.0000 chunk 501 optimal weight: 8.9990 chunk 279 optimal weight: 0.9980 chunk 50 optimal weight: 0.0060 chunk 199 optimal weight: 1.9990 chunk 316 optimal weight: 20.0000 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS C 421 GLN D 226 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 50319 Z= 0.153 Angle : 0.570 9.215 68016 Z= 0.292 Chirality : 0.045 0.319 7563 Planarity : 0.004 0.057 8982 Dihedral : 4.907 35.202 6855 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.63 % Allowed : 7.98 % Favored : 91.39 % 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: -1.46 (0.11), residues: 6279 helix: -0.83 (0.11), residues: 2289 sheet: -1.68 (0.19), residues: 729 loop : -0.78 (0.12), residues: 3261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 551 HIS 0.007 0.001 HIS 3 300 PHE 0.017 0.001 PHE B 674 TYR 0.034 0.001 TYR F 244 ARG 0.005 0.000 ARG D 313 *********************** 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 346 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 312 time to evaluate : 4.297 Fit side-chains revert: symmetry clash REVERT: A 442 MET cc_start: 0.7479 (mpp) cc_final: 0.7233 (mpp) REVERT: A 449 MET cc_start: 0.6964 (tpp) cc_final: 0.6720 (tpp) REVERT: B 158 MET cc_start: 0.5692 (mmm) cc_final: 0.5279 (pmm) REVERT: E 427 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6451 (ppp) REVERT: E 442 MET cc_start: 0.7504 (mpp) cc_final: 0.5302 (tpt) REVERT: E 652 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6925 (t) REVERT: E 740 MET cc_start: 0.7880 (mmm) cc_final: 0.7506 (mmm) REVERT: C 442 MET cc_start: 0.7540 (mmm) cc_final: 0.6780 (mmt) REVERT: 2 250 LEU cc_start: 0.1962 (OUTLIER) cc_final: 0.1696 (pp) REVERT: 3 174 HIS cc_start: 0.1232 (m-70) cc_final: 0.0845 (m-70) REVERT: 3 254 GLN cc_start: -0.0887 (mt0) cc_final: -0.2213 (mm-40) REVERT: 3 417 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.4704 (mmt) REVERT: 1 180 TYR cc_start: 0.4025 (OUTLIER) cc_final: 0.3221 (t80) REVERT: 1 254 GLN cc_start: -0.1216 (mt0) cc_final: -0.2189 (mm-40) outliers start: 34 outliers final: 19 residues processed: 332 average time/residue: 0.4329 time to fit residues: 254.8599 Evaluate side-chains 297 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 273 time to evaluate : 4.267 ------------------------------------------------------------------------------- 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 344 MET Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 292 GLU 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 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 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 250 LEU 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 582 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 343 optimal weight: 4.9990 chunk 440 optimal weight: 0.9980 chunk 341 optimal weight: 6.9990 chunk 508 optimal weight: 5.9990 chunk 337 optimal weight: 0.9980 chunk 601 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 568 GLN F 340 HIS F 568 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 50319 Z= 0.232 Angle : 0.578 8.473 68016 Z= 0.294 Chirality : 0.046 0.298 7563 Planarity : 0.004 0.055 8982 Dihedral : 4.838 41.526 6855 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.78 % Allowed : 8.45 % Favored : 90.77 % 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: -1.40 (0.11), residues: 6279 helix: -0.76 (0.11), residues: 2289 sheet: -1.61 (0.19), residues: 714 loop : -0.77 (0.12), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 580 HIS 0.005 0.001 HIS 3 300 PHE 0.020 0.001 PHE D 674 TYR 0.032 0.001 TYR B 244 ARG 0.009 0.000 ARG 3 252 *********************** 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 319 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7060 (tpp) cc_final: 0.6832 (tpp) REVERT: B 158 MET cc_start: 0.5745 (mmm) cc_final: 0.5293 (pmm) REVERT: E 427 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6408 (ppp) REVERT: E 442 MET cc_start: 0.7502 (mpp) cc_final: 0.5222 (tpt) REVERT: E 652 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.7039 (t) REVERT: E 740 MET cc_start: 0.7899 (mmm) cc_final: 0.7470 (mmm) REVERT: F 340 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5868 (t-90) REVERT: C 442 MET cc_start: 0.7504 (mmm) cc_final: 0.6726 (mmt) REVERT: 2 250 LEU cc_start: 0.1929 (OUTLIER) cc_final: 0.1710 (pp) REVERT: 3 180 TYR cc_start: 0.3938 (OUTLIER) cc_final: 0.2569 (t80) REVERT: 3 254 GLN cc_start: -0.0813 (mt0) cc_final: -0.2099 (mm-40) REVERT: 3 417 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.4667 (mmt) REVERT: 3 493 ASN cc_start: 0.5153 (p0) cc_final: 0.4686 (m-40) REVERT: 1 180 TYR cc_start: 0.3980 (OUTLIER) cc_final: 0.3229 (t80) REVERT: 1 254 GLN cc_start: -0.1191 (mt0) cc_final: -0.2173 (mm-40) outliers start: 42 outliers final: 26 residues processed: 304 average time/residue: 0.4316 time to fit residues: 231.9458 Evaluate side-chains 300 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 4.311 ------------------------------------------------------------------------------- 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 309 ILE Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 509 THR 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 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 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 292 GLU Chi-restraints excluded: chain C residue 342 ILE 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 250 LEU Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 180 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 359 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 118 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 chunk 382 optimal weight: 30.0000 chunk 409 optimal weight: 0.6980 chunk 297 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 472 optimal weight: 40.0000 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 HIS B 568 GLN F 340 HIS F 568 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2526 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= 0.170 Angle : 0.564 8.771 68016 Z= 0.287 Chirality : 0.045 0.315 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.734 41.737 6855 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.76 % Allowed : 8.71 % Favored : 90.53 % 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: -1.27 (0.11), residues: 6279 helix: -0.62 (0.11), residues: 2286 sheet: -1.53 (0.20), residues: 699 loop : -0.73 (0.12), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 580 HIS 0.028 0.001 HIS F 340 PHE 0.019 0.001 PHE D 674 TYR 0.025 0.001 TYR B 244 ARG 0.006 0.000 ARG F 338 *********************** 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 319 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 278 time to evaluate : 4.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.6991 (tpp) cc_final: 0.6766 (tpp) REVERT: B 158 MET cc_start: 0.5845 (mmm) cc_final: 0.5346 (pmm) REVERT: E 442 MET cc_start: 0.7488 (mpp) cc_final: 0.5287 (tpt) REVERT: E 652 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.7049 (t) REVERT: E 740 MET cc_start: 0.7840 (mmm) cc_final: 0.7369 (mmm) REVERT: C 442 MET cc_start: 0.7513 (mmm) cc_final: 0.6725 (mmt) REVERT: 2 250 LEU cc_start: 0.2331 (OUTLIER) cc_final: 0.2077 (pp) REVERT: 3 180 TYR cc_start: 0.3951 (OUTLIER) cc_final: 0.3020 (t80) REVERT: 3 254 GLN cc_start: -0.0637 (mt0) cc_final: -0.1937 (mm-40) REVERT: 1 180 TYR cc_start: 0.3926 (OUTLIER) cc_final: 0.3200 (t80) REVERT: 1 254 GLN cc_start: -0.1187 (mt0) cc_final: -0.2186 (mm-40) outliers start: 41 outliers final: 25 residues processed: 305 average time/residue: 0.4422 time to fit residues: 237.3670 Evaluate side-chains 296 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 267 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TYR 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 309 ILE Chi-restraints excluded: chain B residue 344 MET 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 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 757 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 309 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 250 LEU Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 180 TYR Chi-restraints excluded: chain 1 residue 180 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 7.9990 chunk 576 optimal weight: 20.0000 chunk 525 optimal weight: 20.0000 chunk 560 optimal weight: 7.9990 chunk 337 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 440 optimal weight: 3.9990 chunk 171 optimal weight: 0.0870 chunk 506 optimal weight: 6.9990 chunk 530 optimal weight: 50.0000 chunk 558 optimal weight: 0.0010 overall best weight: 2.2170 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 50319 Z= 0.285 Angle : 0.606 8.837 68016 Z= 0.306 Chirality : 0.047 0.312 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.823 45.044 6855 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.78 % Allowed : 8.82 % Favored : 90.40 % 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: -1.33 (0.11), residues: 6279 helix: -0.68 (0.11), residues: 2298 sheet: -1.58 (0.20), residues: 699 loop : -0.75 (0.12), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.005 0.001 HIS 1 300 PHE 0.032 0.001 PHE D 674 TYR 0.028 0.001 TYR F 244 ARG 0.007 0.000 ARG F 358 *********************** 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 317 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 HIS cc_start: 0.6311 (OUTLIER) cc_final: 0.5574 (t70) REVERT: A 449 MET cc_start: 0.7064 (tpp) cc_final: 0.6807 (tpp) REVERT: B 158 MET cc_start: 0.5850 (mmm) cc_final: 0.5312 (pmm) REVERT: E 442 MET cc_start: 0.7496 (mpp) cc_final: 0.5313 (tpt) REVERT: E 740 MET cc_start: 0.7854 (mmm) cc_final: 0.7338 (mmm) REVERT: F 340 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.5922 (t-90) REVERT: C 340 HIS cc_start: 0.6300 (OUTLIER) cc_final: 0.5436 (t70) REVERT: C 442 MET cc_start: 0.7553 (mmm) cc_final: 0.6793 (mmt) REVERT: C 720 MET cc_start: 0.5266 (ttp) cc_final: 0.5025 (ttp) REVERT: 3 180 TYR cc_start: 0.3944 (OUTLIER) cc_final: 0.2997 (t80) REVERT: 3 254 GLN cc_start: -0.0646 (mt0) cc_final: -0.1950 (mm-40) REVERT: 1 180 TYR cc_start: 0.3919 (OUTLIER) cc_final: 0.3215 (t80) REVERT: 1 254 GLN cc_start: -0.0879 (mt0) cc_final: -0.1993 (mm-40) outliers start: 42 outliers final: 32 residues processed: 300 average time/residue: 0.4556 time to fit residues: 242.0510 Evaluate side-chains 305 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 268 time to evaluate : 4.316 ------------------------------------------------------------------------------- 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 344 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 292 GLU 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 F residue 757 MET 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 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 447 VAL 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 3 residue 180 TYR Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 0.6980 chunk 592 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 411 optimal weight: 2.9990 chunk 621 optimal weight: 3.9990 chunk 572 optimal weight: 30.0000 chunk 495 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 382 optimal weight: 40.0000 chunk 303 optimal weight: 0.0170 overall best weight: 1.4422 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50319 Z= 0.210 Angle : 0.580 8.649 68016 Z= 0.294 Chirality : 0.046 0.304 7563 Planarity : 0.004 0.057 8982 Dihedral : 4.758 44.147 6855 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.63 % Allowed : 9.08 % Favored : 90.29 % 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: -0.62 (0.11), residues: 2301 sheet: -1.54 (0.20), residues: 699 loop : -0.74 (0.12), residues: 3279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 551 HIS 0.005 0.001 HIS 1 300 PHE 0.039 0.001 PHE D 674 TYR 0.028 0.001 TYR F 244 ARG 0.007 0.000 ARG F 338 ********************** 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 fitting. rotamer outliers: 34 poor density : 274 time to evaluate : 4.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7017 (tpp) cc_final: 0.6739 (tpp) REVERT: B 158 MET cc_start: 0.5850 (mmm) cc_final: 0.5305 (pmm) REVERT: E 442 MET cc_start: 0.7477 (mpp) cc_final: 0.5271 (tpt) REVERT: C 442 MET cc_start: 0.7502 (mmm) cc_final: 0.6784 (mmt) REVERT: C 720 MET cc_start: 0.5258 (ttp) cc_final: 0.5019 (ttp) REVERT: 3 180 TYR cc_start: 0.3929 (OUTLIER) cc_final: 0.3008 (t80) REVERT: 3 254 GLN cc_start: -0.0830 (mt0) cc_final: -0.2054 (mm-40) REVERT: 1 180 TYR cc_start: 0.3695 (OUTLIER) cc_final: 0.3234 (t80) REVERT: 1 254 GLN cc_start: -0.0733 (mt0) cc_final: -0.1984 (mm-40) outliers start: 34 outliers final: 29 residues processed: 295 average time/residue: 0.4476 time to fit residues: 233.4253 Evaluate side-chains 300 residues out of total 5352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 269 time to evaluate : 4.334 ------------------------------------------------------------------------------- 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 344 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 292 GLU 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 344 MET Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 292 GLU 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 731 ILE Chi-restraints excluded: chain 2 residue 180 TYR Chi-restraints excluded: chain 2 residue 417 MET Chi-restraints excluded: chain 3 residue 180 TYR Chi-restraints excluded: chain 1 residue 180 TYR Chi-restraints excluded: chain 1 residue 261 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 0.7980 chunk 527 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 456 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 495 optimal weight: 0.6980 chunk 207 optimal weight: 0.0370 chunk 509 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 ** 2 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 436 HIS 2 619 ASN ** 3 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 619 ASN ** 1 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 436 HIS 1 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.188997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.137669 restraints weight = 122494.710| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.39 r_work: 0.3458 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 50319 Z= 0.153 Angle : 0.556 8.742 68016 Z= 0.282 Chirality : 0.045 0.284 7563 Planarity : 0.004 0.056 8982 Dihedral : 4.552 42.085 6855 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.65 % Allowed : 9.15 % Favored : 90.19 % 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: -1.07 (0.11), residues: 6279 helix: -0.44 (0.11), residues: 2307 sheet: -1.41 (0.20), residues: 675 loop : -0.65 (0.12), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.005 0.001 HIS 1 300 PHE 0.027 0.001 PHE D 674 TYR 0.021 0.001 TYR F 244 ARG 0.005 0.000 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7822.62 seconds wall clock time: 139 minutes 56.49 seconds (8396.49 seconds total)